How to remove unused folders created by apps?
Unfortunately, as the comments state, there is currently no way to automate this - and I for one wish there was, as I find myself deleting loads of folders as well.

You should do it manually - but methodically, and it starts to seem to take a lot less time, as you start to think about it.

One thing to look out for is folders for game apps that you installed, as they may contain the downloaded game data - which can be quite large, which you may wish to keep incase you want to install and play the game again.

Like Izzy mentioned, SD Maid finds some of the orphan files for you - but not all.