Working on the fact that the C: usually has the OS on it. I am going to asume you intend to re-install Win2K on your C:.
If this is the case then boot from your Win2K CD-Rom and during the DOS based part of the installer, you will be given the option to delete, create and format partitions as either Fat32 or NTFS.
If you want to install a different OS, then I would recommend you boot from a Windows 98se floppy disk and use fdisk to delete / create the partition. (Don't forget to make the partition active if you wish to install an OS on to it.)
Then use the Format C: to make the drive useable. (The Format command is part of the RAMDisk which will be set to a different drive letter, not A:.) Note that if the partition is bigger than 2045 Mb (2.04Gb), then it will be formatted as Fat32. The DOS Format command doesn't support the NTFS file system.
Remember that if you need advise on DOS commands, you can use the help switch ' /?' as follows C:\><command> /?
Hope that helps.
Barry.