Cut shape out from above paths (automated) in Illustrator

Is it possible to delete parts that overlap a underlying shape (on a underlying group/layer).

To illustrate the question:

Each shape is in it's own group, "1" on the bottom and "4" on top.

Starting point:

I want to delete every part that overlaps on the underying shape. For example: The "2" and the "4" are on top of the "1", so the parts on the "1" that overlaps the "2" and the "4" must be deleted. While the "4" also cuts the "2". The "4" itself remains untouched, because it is on top and no other path/shape is above it. The same goes for the "3".(See images below)

Of course for this simple tasks you can use the Pathfinder tools, but this would be unmanageable for bigger documents with a lot of paths. This has to be done for all of the paths. Is there any way that can speed up the process, or automate it.

I hope this is a bit clear. Please tell me if it is not, I'll try to explain it differently.