What do you mean by 'cleanup'? - If you moved the indexes to another location, simply adjust the index pathname (from the client name)and delete the old directories.
If you want to physically compress the databases, this was only necessary until NW 5.x . Since version 6, obsolete file index data is deleted automatically. The only way to cut the indexes is to shrink the browse time.
If you need more space and you must keep the current indexes, you may either relocate them or simply add more disk space.