I did this very same thing on my computer the first time I tried to install Windows XP Pro. Installation was carried out from within the old Windows 2000 environment and it did go well. I had chosen fresh install and ( that was the intention as I had bought a copy of WINDOWS XP PRO FULL VERSION and wanted to wipe out the old install...I do not believe in UPGRADE Versions!). But when rebooted I saw multiple boot option and soon figured out that installation did not go as I had expected... ..To clean it I had to go into boot.ini file and delete entry corresponding to Windows 2000. Also based on my experience of old directory structure, I had to manually delete those. I could easily remove the WINNT directory as it belonged to Windows 2000. Difficult task was the program files directory as it has old as well as new stuff mixed up. I used date and timestamp sorting to figure out what was old and not needed but you be very careful here.
IMPORTANT NOTE: If you remove a program file belonging to Windows by mistake, you may be heading for trouble !
