FAT32 provides for no security at all. NTFS on the otherhand, allows for setting permissions on select folders and files.
FAT32 is compatible with Windows 95/98/Me and can be written to by Linux users as well. NTFS is only usable to Windows NT users (2K/XP/etc.) and will only allow Linux users to read the contents of the drive.
NTFS makes better use of the alloted drive space. FAT32 also has limitations on individual file sizes which can be problematic when working with video content.
NTFS is simply more stable and has a better instance of reliability than FAT32.
Converting a partition from FAT32 to NTFS can be done by an inbuilt utility in the Windows XP operating system — but it is important to realise that it is a one-way process. You cannot convert back, except possibly by use of Partition Magic 7.01, and that is not always successful. Windows XP has no tool for converting from NTFS to FAT32.
There are a couple of things to do in advance if the conversion is to be efficient. If you do not take these preliminary steps, you are liable to end up with only 512 byte clusters, which is not a good idea.
What happens is that FAT32 partitions formatted by most Windows versions except Windows XP itself (and possibly Windows 2000) have an odd multiple of 2 kilobytes in the “system” sectors before the data area, where the File Allocation Tables themselves and clustering start. Therefore, clusters 4 KB in size are not aligned on 4 KB boundaries, as NTFS will want. CONVERT.EXE, finding it cannot use 4K clusters, gives up and makes the clusters only 512 bytes (one half KB) instead. (For a table of the varying default cluster sizes used by FAT16, FAT32, and NTFS for partitions of varying sizes, click here.)
It is, therefore, important to realign the partition before conversion, by moving all the data area up to a 4K boundary. (This will absorb odd sectors at the far end which otherwise would not get used). You can use BootIT NG, from BootitNG.com. This is a shareware program, priced at US$30 but with a 30-day fully functional trial, which allows for the conversion.
Download the BOOTITNG.ZIP file to its own folder, extract the contents of the ZIP file, then run BOOTITNG.EXE, which will make a bootable floppy. Boot this floppy. For purposes of Partition Management, there is no need to install the program to hard disk, so click Cancel Install, thus entering Maintenance. Click Partition Work. Highlight the partition you intend to convert. Click Slide, which has an option check box to Align for NTFS only. Click OK. As it has to move almost every sector on the entire partition, this will take a very long time — schedule it for a meal break, or start it to run overnight. (If it finishes quickly, that probably means that the partition was properly aligned already.)
Then restart the computer, boot Windows XP, being sure to logon as an Administrator, and defragment the disk. This ensures that there is, as far as possible, a contiguous area for the NTFS Master File Table. It is best if there is a fairly substantial amount of free space while you do it.
Now use the Windows XP convert tool: Go to Start | All Programs | Accessories | Command Prompt (or, from a Run box, type CMD) and, assuming you intend to convert C:, give the command:
Note the name of the disk in the first line, and the Volume Serial Number (for example, 3F4E-2D1B) in the second. Then type:
CONVERT C: /FS:NTFS
It will ask for that name in confirmation. Then it will ask two further questions. Reply Y each time to set up conversion to happen at the next boot, then restart the machine. (If you are converting a partition other than the operating system’s partition, you may find that it runs without rebooting.) After returning to Win XP, the hard disk will work for two or three minutes, tidying up. Leave things alone during this time.