You can convert from FATxx to NTFS on the fly. (you cannot convert back) It will rebuild the file system next time you reboot. There is a restriction in so far as there must be enough free space on the partitions you are converting. If it is too small it will tell you so it's pretty foolproof.
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.
So you would type in at a dos prompt :-
"convert c: /FS:NTFS"
Bests
Martin