I have some custom portraits installed. But the game has created a lot more folders than I currently need.

It's annoying to have to click through all these. Is there an efficient way to prune them down?

What I do is rename the portrait folders I will be using, so when the game creates more 'default' custom portraits, I just delete them. You can access the folders easily from the game itself - during Custom portrait selection you can click on 'Open portrait folder', and just go one folder back in the directory.