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When using Windows 2000 or XP, you do not have to wipe out a FAT partition to convert it to NTFS. They both include a program called convert in the windowssystem32 directory.
C:WINDOWSsystem32>convert /? Converts FAT volumes to NTFS. CONVERT volume /FS:NTFS [/V] [/CvtArea:filename] [/NoSecurity] [/X] volume Specifies the drive letter (followed by a colon), mount point, or volume name. /FS:NTFS Specifies that the volume is to be converted to NTFS. /V Specifies that Convert should be run in verbose mode. /CvtArea:filename Specifies a contiguous file in the root directory to be the place holder for NTFS system files. /NoSecurity Specifies the converted files and directories security settings to be accessible by everyone. /X Forces the volume to dismount first if necessary. All opened handles to the volume would then be invalid.
By doing a "c:windowssystem32convert c: //fs:ntfs", the system will convert c: to a NTFS on the next reboot. The option to do this also shows up when you upgrade Windows 2000 or XP.