Well, all NT files are stored in the WINNT directory, so if you really wanted to you could just delete the C:\Windows directory, which is the same thing but for win 98/me.
A better option if you have the hard drive space to spare is to just shorten the amount of time you have at boot up to choose OS' to say 8 seconds or so, and just live with knowing me is there. Just in case you have win 2k problems and have no way to get in. IF you use NTFS you can forget this one though. Win 98/me can't read NTFS partitions, and if you have NTFS then you have to have 98/me on another partion anyway. Well, hope I helped some!
LUCK!!!