There's no easy answer. You'll have to do it one person at a time. Most of us have been there when we were first starting out. I've found that if you start with people at the far end of the branches, with the oldest ancestors, and then work forward in time this helps. If you have no source data for a person except another member tree then I would consider deleting them completely.
The best way to not have this happen is to not merge from other trees.