NTFS Bootdisk

I’m running NT 4.0 SP6 & IIS 4.0 as my Web server. I’ve had a hacker install a program into cgi-bin folder that shows no name. I’ve tried to delete it with no luck. I tried to bring up a DOS window to delete the cgi-bin folder, but DOS will not work. How do I make an NTFS boot disk to not let this rouge program load into memory so I can delete the cgi folder???