I had posted a project that I had used muriatic acid to clean some of the pieces. Here is a web site that uses a process that is not as caustic but it still does a good job on the rust. Hock Tools tells of the same process but this website give a few more details of how this process works and some of the cautions you should have.
For cleaning things with a buildup of trash (dirt, sawdust etc.) like the teeth on a file, the muriatic acid (this is used in cleaning swimming pools you can get it at most hardware stores) is still the easiest and fastest way I know of to deep clean these tools. USE CATION WITH ANY ACID!! I have taken old files and soaked them for about 5 min. and then clean them off with a solution of Arm and Hammer Baking Soda to neutralize the acid, and then I rinse off with clean water. Make sure you blow off any excess water because this metal will be clean and will start rusting up fast if left to air dry.
There are alot of ways to clean rust hope this helps.