Are you reinstalling? To do a clean install, either boot the Windows NT
install CD-Rom or setup disks. When you get to the point, delete the
existing NTFS and or other partitions found. After you delete the
partition(s) abort  the install, then
again restart the pc booting the CD-Rom or setup disks to avoid unexpected
drive letter assignments with your new install.

Depending on your drive's geometry Windows NT supports a system partition
(the first primary active partition and where the files required to start
the OS reside (boot sector)) limited to 7.8gB NTFS or 4gB Fat16, while the
boot partition (where the OS is installed) is not limited in size. You wont
be able to create a system partition greater than 4gB with Windows NT Setup;
if you need a system partition 4gB - 7.8 gB, you'll need to use Partition
Magic or use another NT machine to create the first primary active
partition. The system and boot partition can be the same partition.

If you created one large system/ boot partition > 7.8 gB and installed the
OS, it may work, but the problem is if you defragment the drive or service
pack the install and the files ntdetect.com, ntldr, boot.ini, and
ntbootdd.sys end up being relocated to a point beyond the 7.8 gB barrier,
then the bootstrap process wont be able to find them and the OS wont start.

Once the OS is installed you can use Disk Administrator to partition and
format the rest of your drive. You'll need atapi.sys from SP4 or later for
Windows NT to be able to recognize a drive larger than ~ 8 gB. See the first
article for the link and instructions.

Installing Windows NT on a Large IDE Hard Disk
http://support.microsoft.com/default.aspx?scid=KB;en-us;q197667

Windows NT 4.0 Supports Maximum of 7.8-GB System Partition
http://support.microsoft.com/default.aspx?scid=KB;en-us;q224526

Boot Partition Created During Setup Limited to 4 Gigabytes
http://support.microsoft.com/default.aspx?scid=KB;en-us;q119497

Windows NT Partitioning Rules During Setup
http://support.microsoft.com/default.aspx?scid=KB;en-us;q138364

Loading MS-DOS is not the way to reinstalling NT.
If you needed access to a FAT volume from DOS a simple boot
diskette would have been fine, installing MS-DOS was
unnecessary.  Also using the MS-DOS version of FDISK or
FORMAT can munge things up as it doesn't support such
things as FAT volumes over 2 GB and Long File names.
Also Windows NT uses it's own, special bootsector and
bootloader.  Windows NT is NOT built on top of MS-DOS!