Trim with region

Hi,

I'm trying to trim a certain amount of lines with a series of circles, both are organized in trees with the same structure so it should work, I think the problem is there are some empty branches in one of the trees (the one with lines) so it appears as if the trees had different lenghts.

I think it could help if I could extract the branch index from the empty branches from one tree and remove those branches from the other one, so both would have the same amount of branches, but maybe there is a better way. Any suggestions?