As you know FAT file systems offer very little in the way of security. Therefore its always wise to format your drives to use the NTFS file system, where you gain the ability to control access to files and directories on a per user basis.
While formatting a drive to NTFS is straight-forward work, performing that conversion during an unattended installation of Windows NT may not be straight forward for you.
To convert a FAT file system to NTFS during an unattended installation, first copy the I386 or Alpha directory from the installation CD onto your hard disk. These instructions assume you copied the I386 from the CD to the I386 directory on your hard disk.
Expand the file I386\INITIAL.IN_ to I386\INITIAL.INF. Once expanded, rename the I386\INITIAL.IN_ to I386\INITIAL.BK_. Edit the SetAcls section of the I386\INITIAL.INF file, changing the line "set Convert_Winnt = $($1)" to "set Convert_Winnt = YES". Now save the file and run the unattended installation, where the file system will be converted to NTFS during the installation process