Illustrator: Cutting paths from lines

Background: I'm using illustrator to add color to a floor plan imported from a CAD program. The issue I'm running into is that in our CAD, our doors are created by "blocks"and the lines of the walls are covered up by a "wipeout" object in autocad which is imported into Illustrator as a box with a white background and no stroke. It works fine for doing a black and white image but if I place color behind the linework, I have white boxes where all my doors are. I can manually cut the lines, etc which works for small plans but when doing potentially dozens of doors it becomes overly tedious.

I've tried searching, experimenting with the pathfinder, clipping masks, etc but I haven't found anything that works for me. Is there anything that will cut multiple shapes from multiple lines? I attached an image of an example showing the lines of the wall and the boxes of the "wipeout" that I'd like to subtract from walls so there is no white box in front of the color.