Can not delete a file . 4 vh-crew

I think a hacker got into our Windows 2000 system. There is a folder inside one of our websites called “. 4 wg crew” and another called “tagged” in our _vti_log folder. I have managed to remove everything in the site ecept for these folders. I keep getting “cannot read from source file or disk” errors. I am logged in as adminsistrator. I can not boot in safemode. Each time I try, the computer re-boots into normal mode. Can anyone help me? Please Thanks