Presumably your reference to Windows 9x is Windows ME.
Is your Windows ME is on your C partition, and your Windows 2000 installed on a separate partition? And you created the dual boot using Windows 2000's own boot manager, without using third party software?
If so, prepare a Windows Me startup floppy. Restart the computer with floppy. At the A:> prompt, type "sys c:" without the quotation marks, and press Enter. You should then get a message "system transferred". Remove the floppy and restart the computer. You should boot straight into Windows Me, without the OS selection screen.
Once in Windows ME again, you can delete the Windows 2000 system files under your C drive. They are ntldr, ntdetect.com, boot.ini, bootsect.dos, pagefile.sys (ME has its own swap file).
You can then reformat the Windows 2000 partition and use it as you like.
If your dual boot is set up differently from my assumptions above, post back.
This thread is now locked and can not be replied to.