FEI Scios 2 Mounting instructions

User Operation Manual
Edition 1
Mar-2017

FreeRTOS Licensing Information
This product contains FreeRTOS software. Upon request, FEI Company will provide you with the FreeRTOS source code
and any modifications to the FreeRTOS source code made by FEI.
Trademark Acknowledgments
FEI logo is a trademark of FEI Company.
FEI is a registered trademark of FEI Company.
Microsoft® and Windows 7 are registered trademarks of Microsoft Corporation.
FreeRTOS™, FreeRTOS.org™ and the FreeRTOS logo are trademarks of Real Time Engineers Ltd.
This manual was produced using FrameMaker™ document publishing software.
FrameMaker™ and Adobe are registered trademarks of Adobe Systems Incorporated.
Other product and company names mentioned herein may be trademarks of their respective owners.
Copyright © 2017 by FEI Company
The information and materials contained herein are confidential and proprietary to FEI Company.
They are provided for your organization's internal use on a need-to-know basis.
They cannot be duplicated or disseminated for any third party without the express consent of FEI Company.
Limited Rights
The following notice applies to the U.S. Government and other purchases with federal funds:
Contractor Name:
FEI Company
Contractor Address:
5350 NE Dawson Creek Drive, Hillsboro, Oregon 97124, USA
The Government's rights to use, modify, reproduce, release, perform, show, or disclose these technical data
are restricted to those rights specified in:
DFARS 252.227-7015(b)(2), FAR 52.227-14(g)(2) (Alternate II) and FAR 12.211.
Any reproduction of technical data or portions thereof marked with this legend
must also reproduce the markings.
Any person, other than the Government, who has been provided access to such data,
must promptly notify the above named Contractor.
Manufacturer & Technical support
FEI Company, 5350 NE Dawson Creen Drive, Hilsboro, Oregon 97124, USA
www.fei.com

CONFIDENTIAL – FEI Limited Rights Data C-i
Table of Contents
Chapter 1 System Overview
User Manuals . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-1
FEI Microscope Systems Safety Manual. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-1
User Operation Manual . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-1
System Capabilities. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1-2
System Performance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-2
Chapter 2 System Control
System Layout . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-1
Other Software and Hardware . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-1
Interface Elements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-2
Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-2
Hardware . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-2
Mains Switchboard . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-4
System States . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-5
System Startup . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-6
Overnight and Standby . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-7
System Shutdown . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-9
Vacuum System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-10
Vacuum Status . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-11
Vacuum Modes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-12
Equipment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-14
Detector Types and Application . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-14
Stages and Accessories . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-15
Chapter 3 Software Control
Software Interface Elements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-1
Icons. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-1
Tool-Tips . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-1
Pull-down Menus . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-1
Command Buttons . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-2
Property Editor. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-2
Edit Boxes. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-2
Radio Buttons / Check Boxes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-2
Adjusters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-3
2D Controls. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-4
Modules. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-4
Dialogs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-4
Tabs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-4
Progress Bars. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-4
xT microscope Server Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-5
Microscope Control Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-6
Workspace customization . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-6
Menu Bar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-9
Toolbar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-23
Imaging Area. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-27
Status Bar. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-29
Control Pages and Modules . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-30
Preferences Dialog . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-39
FEI Account Manager application . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-50
Accounts control . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-50
User Logins and Account Settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-53

Table of Contents
CONFIDENTIAL – FEI Limited Rights Data
C-ii
Entering Commands in Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-54
Using Mouse . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-54
Using Keyboard . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-55
Chapter 4 Alignments
Common Rules . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-1
Buttons and Control Elements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-1
Alignments List. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-2
Automatic Alignments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-3
Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-4
Magnification Correction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-5
E-Column: Aperture Selection . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-6
E-Column: Preventive Maintenance. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-7
E-Column: Supervisor Alignments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-8
100 – ION: Source Control . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-14
I-Column: Aperture Management . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .4-16
I-Column: Manual Beam Alignment. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .4-17
I-Column: Alignments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .4-18
Stage Alignments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-20
154 – Water Bottle Venting . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .4-21
Plasma Cleaning / External Plasma Cleaning . . . . . . . . . . . . . . . . . . . . . . . . . 4-22
Pump Buffer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .4-23
Vacuum Actions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-24
254 – GIS Alignment (option) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-25
Chapter 5 Operating Procedures
Specimen Preparation and Handling . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-2
Needed Items. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-2
Natural specimen . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-2
Coated Specimen . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-2
Mounting Specimen on Holder . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-2
Specimen Baking Unit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-3
Microscope Control . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-6
Operation Pre-Check . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-6
Inserting / Exchanging Specimen . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-7
Selecting Vacuum Mode . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-7
Imaging Onscreen . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-8
Optimizing Imaging . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-9
Principles of SEM Imaging . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-9
Magnification. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-9
Scan Speed . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-10
Contrast & Brightness . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-10
Focusing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-11
Correcting Astigmatism . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-11
Direct Adjustments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-12
Digital Imaging Enhancement / Imaging Mixing / Coloring . . . . . . . . . . . . . . . . . . . . . 5-14
Accelerating Voltage and Beam Currents . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-16
Column Use Cases. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-18
Standard Detectors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5-19
Everhart Thornley Detector (ETD) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-19
Infrared CCD Camera . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-19
Low Vacuum Detector (LVD) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-20
Trinity Detectors T1 / T2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-21
T1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-21
T2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-21
T3 (option) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-21
Capturing and Handling Single Image. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-22

Table of Contents
CONFIDENTIAL – FEI Limited Rights Data C-iii
Image Types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-22
Saving / Opening / Printing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-23
Recording Movies (Saving Multiple Images) . . . . . . . . . . . . . . . . . . . . . . . . . . 5-24
Movie Settings Dialog . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-24
Movie Procedure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-26
Movie Creator . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-27
Stage Control . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-30
Eucentric Position . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-30
Software Control. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-32
Stage Related Functions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-36
Patterns / Measurements / Annotations. . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-43
Patterning . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5-44
Patterning Control Module. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-45
Patterns Processing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-48
Advanced Patterning tab Modules . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-50
Gas Injection Module (option) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-52
Application Files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-53
Milling. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-55
Viewing Cross Sections. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-58
Chapter 6 Maintenance
Cleaning Procedures Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-1
List of Applied Cleaners . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-1
Cleaning Column Parts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-2
Materials and Technique . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-2
Aperture Strip Module . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-3
Removing Aperture Rod . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-3
Replacing Aperture Module . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-3
Installation of Aperture Rod . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-4
Shutter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-4
Exchange procedure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-4
Stage . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-6
Stage Mechanics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-6
Specimen Holders . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-6
Refilling Water Bottle. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-7
Chapter 7 System Options
Manual User Interface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-3
Joystick . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-3
Uninterruptible Power Supply (UPS) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-4
Optional Detectors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-5
Retractable Detectors Control . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-5
Trinity Detector T3 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-5
Ion Conversion and Electron detector (ICE) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-5
Retractable Directional Backscattered Detector (DBS) – 
Angular Backscattered Detector (ABS) / Concentric Backscattered Detector (CBS) . . . . . . . 7-6
Optional detectors connection . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-7
Directional Gaseous Analytical Detector (GAD). . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-8
Retractable Annular Scanning Transmission Electron Microscopy Detector 
(STEM 3 / STEM 3+) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-10
Nav-Cam # . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-12
Capturing Navigation Image Procedure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-12
Energy Dispersive X-ray (EDX) Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-13
High Vacuum. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-13
Low Vacuum EDX Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-13
STEM EDX Analysis. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-13
External Current Measurement (Keithley Picoamper Meter) . . . . . . . . . . . . . . . . . . . 7-14

Table of Contents
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EasyLift . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .7-15
EasyLift Module Control . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-15
EasyLift Display Control . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-16
EasyLift: Needle Exchange / Calibration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-17
EasyLift Basic Procedures. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-19
MEMS – Heating Stage . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-23
MEMS Parts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-23
MEMS Installation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-24
Software Control . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-24
Remote Imaging . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-27
Connection to Microscope PC . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-27
Microscope PC’s Desktop Sharing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-28
Controlling Microscope Remotely. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-28
UMB Stub Holder Kit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .7-28
Beam Deceleration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-29
Detection Principles . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-29
Beam Deceleration Module . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-30
I-Beam Charge Neutralizer. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-32
Using Charge Neutralizer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-32
Quick Loader . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-34
Description . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-34
Installation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-37
Operations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-38
CryoCleanerEC . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-40
Parts and Accessories. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-40
CryoCleaner Operation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-41
Maintenance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-42
Spare Vessel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-42
Plasma Cleaner . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-43
Sample Cleaning Procedure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-44
Chamber Cleaning . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-44
Specimen Holder Kit Option . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-45
Location Positions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-45
Interface Pillar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-45
Torx Drivers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-45
Clamp Stubs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-46
Multi-Holders . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-46

C O N F I D E N T I A L – FEI Limited Rights Data 1-1
1
System Overview
User Manuals
FEI Microscope Systems Safety Manual
The safety manual provides information for personal safety and maintenance procedures while
operating this FEI system.
This manual is required reading for the end user.
User Operation Manual
The User Manual is delivered in the electronic PDF file only. However, it is possible to print parts of the manual if
this is desired.
It is recommended to read the appropriate User Manual section before operating any microscope function. Most
importantly, you should locate the topics necessary to operate the microscope in the proper way to safely achieve
the best results.
The manual is divided into the following chapters:
1. System Overview (this chapter) 
gives overview of the user manuals and system capabilities.
2. System Control 
describes the system hardware (interface elements, vacuum system, system states, equipment).
3. Software Control 
describes the interface that sets and controls system operation, giving the function of each tool, menu item and
control page.
4. Alignments 
explains how to align the equipment to achieve the optimal performance.
5. Operating Procedures 
gives procedures for how to use the system features.
6. Maintenance 
gives allowed step by step cleaning and maintenance procedures.
7. System Options 
explains relevant options that can be integrated into or accessory to the system.
One can take advantage of the searching and navigation possibilities within the PDF file. In addition, the following
conventions are applied:
•A reference to the specific software element is highlighted in italic. For instance: 
“Clear the Stage menu / Beam Shift Reset item.”
•Some software functions use shortcuts, which are given beside the heading in the brackets 
(for instance: Save (Ctrl + S))and in the Help menu / Keyboard Shortcuts.

System Overview: System Capabilities
C O N F I D E N T I A L – FEI Limited Rights Data1-2
System Capabilities
The Scios is a combination of two systems:
•Scanning Electron Microscope (SEM): produces enlarged images of a variety of specimens achieving
magnification over 100 000× providing high resolution imaging in a digital format.
•Focused Ion Beam (FIB) system: capable of fast and precise milling of the specimen material, revealing the
structure under the surface layer, making cross sections, deposition layers, etc. The ion system produces high
resolution images as well.
The integration of both systems yields a powerful analytical tool for obtaining any data from any sample in three
dimensions.
This important and widely used analytical tool provides exceptional field of view, minimal specimen preparation,
and the ability to combine the technique with X-ray microanalysis.
Users can switch between the two beams for quick and accurate navigation and milling. Convergence of the SEM
and FIB at a short working distance allows precision “slice-and-view” cross-sectioning and analysis at high
resolution. The instrument provides optimum throughput, resolution and automation.
FIB/SEM instrument provide an expanded range of capabilities not possible with separate FIB and SEM tools:
•High-resolution electron beam images of FIB cross sections without eroding the feature of interest
•Real-time cross-section images and videos with the electron beam during FIB milling
•Focused electron beam charge neutralization during FIB milling
•High resolution elemental microanalysis of defect cross sections
•Imaging of sample surfaces with the electron beam during navigation without erosion or gallium implantation
from the ion beam
•TEM sample preparation with in situ conductive coating
System Performance
The equipment is intended as a standalone system.
The main instrument components used for imaging of the samples are:
•Electron / Ion source 
The beam of electrons or ions (particles) is emitted within a small spatial volume with a small angular spread
and selectable energy.
•Lens system 
The beam enters the lens system consisting of several electromagnetic or electrostatic lenses and exits to hit
the specimen surface.
•Scan unit 
The scan generator signal, fed to the deflection systems, moves the beam in a raster pattern over the specimen
area. This signal, modulated by the detection system signal produces the onscreen imaging of the specimen
surface.
•Detection unit 
Particles striking the specimen react with atoms of the sample surface in various manners:
– The electron beam produces electrons and photons (X-rays). 
– The ion beam produces ions, electrons and photons (X-rays).
The detector system picks up the particles or photons, converts them into a digital signal which is then sent to
the control PC and shown on the monitor.

System Overview: System Capabilities
C O N F I D E N T I A L – FEI Limited Rights Data 1-3
FIGURE 1-1 Column Schematic Overview
Computer Control
The xT microscope Server and Microscope Control (User Interface) software integrate SEM and FIB functionality
within a Windows 7 operating environment.
This software consists of programs defining specific instrument settings for particular applications, ensuring
reproducibility of complex procedures (for instance imaging, management of image capture, storage, and data
output devices etc.). They also control instrument hardware (the column, detector(s), stage, EDX, vacuum
functions etc.).
Vacuum System
The entire particle path from a source to specimen must be under vacuum so that the particles do not collide with
air molecules.
Various levels of vacuum are necessary, so a Turbo Molecular Pump (TMP) backed by a scroll pre-vacuum pump
(PVP) obtains the necessary specimen chamber pressure.
High Vacuum (HiVac)
This is the conventional operating mode associated with all scanning electron microscopes.
Low Vacuum (LoVac)
In the gaseous mode the electron column is under lower pressure than the specimen chamber. This mode can use
water vapours from a built-in water reservoir, or an auxiliary gas which is supplied by a user and connected to the
gas inlet provided for this purpose. Observation of outgassing or highly charging materials can be made using this
mode without the need to metal coat the sample, which would be necessary for conventional HiVac mode.
Stage
The Scios has a computer-controlled high-accuracy five-axis stage for small samples. It offers precision specimen
computer controlled manipulation and automation of all axes for overall spatial orientation on highly repetitive or
extremely irregular samples.
Specimen exchanges take place through a chamber door which exposes the specimen stage when opened or
through the Quick Loader (option). An exchange time takes a few minutes, with the Quick Loader an exchange is
much more faster. Software and interlocks protect the system against a damage and users against an injury.
Electron / Ion
CONDENSER
LENS(ES)
SCAN GENERATOR M
FINAL LENS
DEFLECTION
SYSTEM
SCAN UNIT
SPECIMEN
DETECTION UNIT
DETECTOR
LENS SYSTEM
Source

System Overview: System Capabilities
C O N F I D E N T I A L – FEI Limited Rights Data1-4
Image Viewing and Capture
Because the amplified detector signal is shown synchronously with the beam scanning, there is a relation between
brightness of an image point on the monitor screen and the signal detected at the corresponding point on the
specimen.
Magnification is the ratio of the size of the viewing monitor screen to the size of the area scanned on the specimen.
Higher magnification is achieved by reducing the size of the area scanned on the specimen.
Beams Control
DualBeam systems ideally position the point of interest for simultaneous ion beam cross-sectioning and electron
beam viewing. Separate scan generators for the two beams permit coupled or independent scan patterns and
magnifications.
Imaging while milling aids in defining milled features. Immediate electron beam images of cross sections are
possible without stage motion or sample transfer. Immediate high resolution SEM imaging after FIB milling also
prevents exposure of milled cross sections to atmospheric contaminants.
Gas Injection System (GIS)
Multiple FEI GIS (option) can be installed for material deposition in conjunction with either electron or ion beam
pattern definition. Electron beam-induced deposition offers the advantage of not sputtering the deposited material
or implanting gallium FIB source ions simultaneously.
The GIS can also contain etching precursor for fast material removal with minimal re-deposition, preferential
etching of cross-section surfaces prior to SEM imaging, and rapid milling of TEM sections.
Several GIS chemistries can be installed on the instrument, depending on a system configuration. This self-
contained apparatus allows the material to be contained entirely within the vacuum system for simple, flexible, and
safe operation.
Analysis Capability
Convergence of the SEM, FIB, and X-ray detection
system (e.g. EDX – Energy Dispersive X-ray – option) at
short working distance allows precision “slice-and-view”
cross-sectioning and chemical analysis at high
resolution of surface and subsurface features.
Various vendor options are compatible with the
instrument (see Chapter 7).