how to delete from history some files, and commits with them?

Hello.

I'm using git for several small projects, and now one of those pgojects have to be divided into two independent parts. So I want to divide git history respectively. I can create two clones and run filter-branch in both to delete files. But I can't find how I may delete empty commits after that. Naturally, I'd prefer to do all process automatically: removing unnecessary files and deleting empty commits without searching to its' hashes.

Can you suggest any solution?