Alas, its something that must be done manually. Tracing out schems from boards is something I have done for a while now - it is tedious, some guesswork can speed it up, but ultimately, a pencil, bit of paper, and a mug of coffee are the tools I used. Normally you can (try) to eliminate subcircuits like power supplies etc.. leaving only the part you're interested in.
With a real board, as suggesting a continuity tester, ohm meter is used. One can also photograph both sides of the board, mirror the bottom, make the top semi-transparent, and overlay them. As for a PCB file, try and get an image for it with different colours for different layers, then eyeball it )