Recently I posted about how to backup your ScanSnap profile settings if you are on the Mac. Here is how to do it on Windows.
The ScanSnap settings are stored in C:\Documents and Settings\yourusername\Application Data\PFU\ScanSnap.
Obviously, “yourusername” would be replaced with your Windows username.
If you can’t see the “Application Data” folder, go up to Tools | Folder Options and set it to be able to see hidden files and folders.

Each of those “PFUSsMon0000x” folders corresponds to one of your profiles, but I would recommend backing up the entire ScanSnap folder.
If you use a backup system like Mozy or Carbonite, make sure you add the ScanSnap folder to be backed up. Otherwise, just copy the folder somewhere.
In case you’re wondering what PFU is, that is a subsidiary of Fujitsu and it is them that developed the ScanSnap.
Hope this helps to protect your ScanSnap settings. Let us know if it does.
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Thank you. The location in Vista and Windows 7 is:
C:Users<User Name>AppDataRoamingPFU
Thanks for letting us know!