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What OS are you going to put on after you format?
If 2000:
If you boot with the Windows 2000 cd, you should have the option for a clean install which should then give you the option to choose which partition to install to (you have one) and then the option to format it.
Otherwise, I don't see why you could boot with a Windows 98 boot disk and run fdisk to delete the partition and then boot with the Windows 2000 cd to install (it can create the partition for you). (There's a small bit of doubt about fdisk on Windows 98 startup disk and NTFS partitions but I'm almost sure you can do it)
 
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