Open any existing FileMaker database with FileMaker Pro. The database has to be on your desktop and not hosted remotely. From the File Menu, select "Save a Copy As..."
Under the Save a Copy As ... options, make sure you select "compacted copy (smaller)". Using the compacted copy method, FileMaker Pro will rebuild a clean copy of your database, repairing and irregularities it finds. This is the best method for cleaning up and repairing and FileMaker database.