Assuming you have 98 on C partition and w2k on another, click here
Do not format the C drive, as the w2k boot files are there.
You can delete all the folders in C. Some of the small files in the C root directory are boot files and other system files for w2k. Those that are not necessary for w2k do not take up much space and so better leave them alone.
To remove the boot options screen, right click C:\boot.ini, Properties, untick Read-only. Click OK. Then open it with Notepad, and edit it to read:
multi(0)disk(0)rdisk(0)partition(2)\WINNT="Microsoft Windows 2000 Professional" /fastdetect
This assumes that w2k is installed on the 1st hard disk, on the 2nd partition on that disk, and in the WINNT directory. The timeout value is irrelevant when you have only one OS.
Save changes and exit. When you reboot, there will be no dual boot option screen, and computer will boot straight into w2k.