Thanks for your comment, I try my best to explain it a little better. I'm not sure yet how a demo project explaining my issue could look like, I think it may be easier if I describe it this way:
I used blender to create a few 3D buildings, which I exported using the better-collada-exporter. I have a folder with all my materials and one .dae file for each building.
Imported in Godot each .dae file is one scene, which is not editable. Inside the scene is one node with one MeshInstance node. I can't create a collision shape in that scene without creating a new inherited scene. That's what I mean by "creating a new scene for each object".
From my camera's view I want to know which building is at a given screen position.
I managed to implement some other things without creating an inherited scene from each of my exported .dae's, so I am looking for a solution that gets this task done without creating new inherited scenes either.