If you upgraded from Windows 98, then you should have an uninstall for Windows 98, if so, do that.
If Win98 is on another partition, and you installed it seperately, see if it's on the uninstall menu.
If it's not uninstallable, edit C:\Boot.ini, and take out the "Windows 98" line, then delete anything you want from the partition Windows 98 is installed on, notably the \WINDOWS dir. If it's on it's own dir, you can take out the other folders you aren't using aswell, like \Program Files