Good question!retro-reviving this thread but out of curiosity, how do you get layer 2 and 3 connections from a scan? I can understand layer 4 and 1 but the internal ones, how does one do that?; with X-Ray or smth?
The short answer is usually you don't, the IIcx is only a 4 layer board with the signals on the outside and power planes in the middle so you only really need to trace the outer layers, the power planes can just be traced out with a multimeter without too much work. Splits in the planes can be a little tricky sometimes but you can usually see these by shining a bright torch through the board
The longer answer is it depends on the board. For boards with a layer count higher than 4 it is often not possible to visually trace the board for the obvious reason of you can't see the traces on the inner layers, sometimes you can use a bright torch but this is often very labour intensive and only really good for following a single trace, it's also common for 6 layer boards to have a signal - power plane - signal - signal - power plane - signal stackup which makes it totally impossible to visually trace without doing what @Kai Robinson suggests and sanding the board down. For these boards I typically just use a multimeter and a conductive brush and map the connections out manually
Though sometimes you just get lucky, some older boards use a very translucent substrate that you can actually see the traces through. I have been working on Radius Rocket clones recently and the substrate on the board I have is so clear I can see all 6 layers of the board just from scans of either side:
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