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The easiest way to go about this is to:
1) Transfer ALL existing data on the drive (Make sure any hidden/system files are included) to another physical or network drive. This will allow the autorun data as well as anything else on the drive to be restored later.
2) Log out of Windows completely and boot to DOS or command prompt.
3) Format the drive using Windows' format utility. From the prompt:
FORMAT x: /FS:NTFS
Where "X" is the letter of the drive.
4) Boot back into Windows. Copy all backup data to the drive.
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