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To convert a volume to NTFS from the command prompt
Open Command Prompt.
In the command prompt window, type
convert drive_letter: /fs:ntfs
For example, typing convert D: /fs:ntfs would format drive D: with the ntfs format.
To open command prompt, click Start, point to All Programs, point to Accessories, and then click Command Prompt.
You can convert FAT or FAT32 volumes to NTFS with this command.
Go to system Help, and search for Convert.
It advises you not to, as it affects performance adversely doing a conversion, as opposed to setting it up as NTFS in the first place.
So the best way would seem to be start all over again, with a fresh installation, using NTFS.
I did it that way and did not suffer any degradation in performance; if anything the opposite. This is from Help
Choosing between NTFS, FAT, and FAT32
You can choose between three file systems for disk partitions on a computer running Windows XP: NTFS, FAT, and FAT32. Use the information below to compare the file systems.
NTFS is the recommended file system for the following reasons:
NTFS is more powerful than FAT or FAT32, and includes features required for hosting Active Directory as well as other important security features. You can use features such as Active Directory and domain-based security only by choosing NTFS as your file system.
It is easy to convert partitions to NTFS. The Setup program makes conversion easy, whether your partitions used FAT, FAT32, or the older version of NTFS. This kind of conversion keeps your files intact (unlike formatting a partition). If you do not need to keep your files intact and you have a FAT or FAT32 partition, it is recommended that you format the partition with NTFS rather than convert from FAT or FAT32. Formatting a partition erases all data on the partition and allows you to start with a clean drive.
Whether a partition is formatted with NTFS or converted using the convert command, NTFS is the better choice of file system. For more information about Convert.exe, after completing Setup, click Start, click Run, type cmd, and then press ENTER. In the command window, type help convert and then press ENTER.
In order to maintain access control on files and folders and support limited accounts, you must use NTFS. If you use FAT32, all users will have access to all files on your hard drive, regardless of their account type (administrator, limited, or standard.)
NTFS is the file system that works best with large disks. (The next best file system for large disks is FAT32.)
There is one situation in which you might want to choose FAT or FAT32 as your file system. If it is necessary to have a computer that will sometimes run an earlier version of Windows and other times run Windows XP, you will need to have a FAT or FAT32 partition as the primary (or startup) partition on the hard disk. Most earlier versions of Windows cannot access a partition if it uses the latest version of NTFS. The two exceptions are Windows 2000 and Windows NT 4.0 with Service Pack 4 or later. Windows NT 4.0 with Service Pack 4 or later has access to partitions with the latest version of NTFS, but with some limitations: It cannot access files that have been stored using NTFS features that did not exist when Windows NT 4.0 was released.
For anything other than a situation with multiple operating systems, however, the recommended file system is NTFS.
Once you convert a drive or partition to NTFS, you cannot simply convert it back to FAT or FAT32. You will need to reformat the drive or partition which will erase all data including programs and personal files on the partition.
That's what it says in the help description for Convert - who am I to argue ;-))
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