The easy part is to determine which parts should be coated. The harder part is making sure the parts that should not be coated do not get coated.
I don't even want to think about the amount of labor and materials I've lost due to conformal coat getting into places where it should not be. Work with your coating supplier to determine the best materials to use when masking your boards. For instance, I recently had an acrylic conformal coat material soak through 3 layers of a "painter's masking tape". Lucky for me, we were able to replace the $80 connector without damaging the $900 PWB it was soldered to.
Every conformal coat material I've used was clear, but had a UV tracer in it so the coating would glow under black light. That means you need a black light to make the coating glow so you can inspect it.
Mike F
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