If you set your BIOS to read your CD drive first when booting, then you can boot from the installation disk. Once there, you should be able to find choices that will allow for you to reformat the drive and install Win2k fresh.
Or worst case... you can use an old Win98 boot disk and remove the NTFS partition, then re-partition the drive and format it that way. Then, when you are installing the Win2k OS, you can tell it to format the partition as NTFS from there.
Either way should work out fine.
Good luck. :)