The Scanning Control options allow you to customize the way SUPERAntiSpyware scans your computer as well as manage Allowed Items and Excluded Folders.

Scanner Options
Ignore files larger than 4MB (recommended)
Ignores files larger than 4MB. Typical spyware files are much smaller than 4MB.
Ignore non-executable files (recommended)
Ignores files that cannot be executed by windows, such as Text documents and Pictures.
Ignore System Restore/Volume Information on ME/XP
On Windows XP and Windows ME, Windows keeps "snapshots" of changes that have occurred on the system so you may revert back to a previous configuration should you encounter a problem at a later date. Spyware/Adware will often be saved in these snapshots and if you revert back to a previous date, this could result in the harmful software being placed back on your computer. Removing items from the snapshots prevents the software from ever being restored if you revert back to a previous date.
Scan only known file types (.exe, .com, .dll, etc.)
Scans only known/typical file types. This speeds the scanning process, but can leave spyware traces on your machine. Generally, traces are not harmful, but may be flagged by other scanners.
Close browsers before scanning
Close Internet Explorer prior to starting the scan. Often times leaving the browser open during a scan can result in additional spyware/adware being installed.
Scan for tracking cookies
Cookies will be scanned for urls of known tracking websites.
Resolve Links/Shortcuts during scan (.lnk)
On some systems attempting to resolve .lnk files using the MSI (Microsoft Installer) API can cause issues. This only occurs under rare circumstances. If SUPERAntiSpyware locks ups or "hangs" during the scan, you may wish to uncheck this option and attempt to scan again.
Terminate memory threats before quarantining
Certain spyware applications will attempt to "crash" your computer when they are terminated. If you have problems or crashes when quarantining and removing spyware, uncheck this option and try the scan and removal process again.
Scan Alternate Data Streams
Alternate Data Streams (ADS) are available on NTFS formatted drives. Certain spyware/malware applications may try and "hide" data in these streams. Enabling this option will increase the scanning time, but may be required for heavily infected systems.
Use Kernel Direct File Access
This option allows SUPERAntiSpyware to use our "kernel direct" technology that can find spyware that attempts to hide itself from the operating system. If you experience problems while scanning, disable this option.
Use Kernel Direct Registry Access
This option allows SUPERAntiSpyware to use our "kernel direct" technology that can find spyware that attempts to hide itself from the operating system. If you experience problems while scanning, disable this option.
Use Direct Disk Access
This option allows SUPERAntiSpyware to bypass the Windows API and access the disk directly so that no file can "hide" from being scanned. This currently works for NTFS volumes only.
Click Manage Allowed Items... and a screen similar to the following will be displayed.

A list of items you have elected to trust will be displayed. If you wish to remove, and thus no longer trust an item, select the item and click Remove. To remove all items from the list, click Remove All.
Excluded Folders
Excluding folders allows you to speed up the scanning process by not scanning folders that may contain lots of files, such as Music files or Pictures, and typically do not contain spyware/adware items. Click Manage Excluded Folders... and a screen similar to the following will be displayed:

A list of folders currently excluded from scanning will be displayed.
Add...
Adds a folder to the list of folders to be excluded during scanning.
Remove
Removes the highlighted (selected) folder from the list.
Remove All
Removes all folders from the excluded list.