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If you want to use Revit for the latest stages of design or during pre-constructio, some tools, specially those to create layer based families like Walls, Floors, Ceilings and Roofs might not work for you. This tools were probably designed to speed up modeling but thinking more of an architect's need (drafting plans) than actually Virtually Building your facility in the computer. This problem has been partially solved with the Create Parts Tool. It is a good improvement appeared in Revit 2013, but it does complicate a bit extracting quantities.
A solution to build the model as it would be build on real life is to model walls (or other layer based elements) in parts. That is, that instead of modelling a brick wall with its layers of substrates and finishes in one element, we model them in several stages.
The main problem with this approach is what to do whit openings. A Window or Door will only cut the wall that actually hosts it, right? Well, not exactly. If you have two parallel walls and place a door in one of them, you can extend the opening cut to the 2nd wall by joining geometry of the two walls. See the pic.