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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). For this, I suggest BootIT NG, from BootitNG.com. This is a shareware program, priced at US$30 but with a 30-day fully functional trial. You may well find it valuable also for its Disk Imaging and Partition Management capabilities.

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:

VOL C:

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.

Consult the Hints in the Windows Product Activation article (under What About Formatting a Hard Disk?) regarding the resetting of the volume serial number, which will have been changed. The hints given will assure that you do not lose a Windows Product Activation “life.”

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For the question above similar to "Can I format my drives without loosing my files?", the answer is absolutely not, formating completely erases the drive. Formating should not be confused with the XP file format conversion tool in XP and other 3rd party apps.

Edit:

Just to add, the floppy created as described above with BootitNG is not time restrictive. I've used it many times to do the above described action plus added partitions to existing drives with no ill affects. If can also be saved to a bootable CD for machines without floppy drives.

MJ