How to Mask 3D Layers while using Cinema 4D Renderer

Have you considered setting up your comp with the classic rendering engine, the lights, the camera moves, and even including all of the textures you want to apply to your extruded shapes, then exporting that comp as a C4D file and doing the extruding in C4D Lite? You have a lot more control over everything. There are a couple of recent threads on the technique and I have posted fairly detailed descriptions of the workflow. You might want to check out this thread: How to create a 3D spaceship hangar?3133

If you want to stick with the C4D rendering option and extruding text and shape layers in AE, then you will have to nest those comps in a standard comp and apply your effects and masks there. It gets a lot more complicated very quickly. 

Pre-compose and set the parent comp renderer to the standard renderer.

Mylenium