To wipe the drive, some ways include; boot a win98 startup disk, run fdisk
and delete all partition information found (as long as NTFS is primary). Or
boot the Windows 2000 CD-Rom or setup disks and when you get to the point,
delete the existing NTFS and or other partitions found, then abort the
install. Or use a utility named delpart. Once removed you can partition and
format the drive as you wish. Boot the Win98 CD-Rom or restore CD-Rom to
start your install.
You can boot with your Win98 startup disk and issue the command
sys C:
this will rewrite the boot sector, then you can delete these files boot.ini,
ntldr, ntdetect.com, bootsect.dos, pagefile.sys and possibly ntbootdd.sys
from the root of the System partition C:\., then you can format D:\