The difference of MSDE to other software is it can be installed on a computer many times, generating a number of installations instance.
uninstall it is easy, through the Start menu -> Control Panel -> Add Remove Programs -> Microsoft SQL Server Desktop Engine (coresponding instance)
select the corresponding MSDE2000 instance to uninstall.

Warning: after the MSDE2000 uninstall, all database belonging to the instance will not be able to continue to use, even if the re-installation of the instance. Please do a backup of database through MSDESQL data backup or maintenance tool in advance.
MSDE2000 uninstall and install again in the original directory that instance data exist might cause error messages. Please delete the original directory before create the database.