Well, I'm not sure what exactly you're talking about "Thermal transfer to PCB". I thought you were speaking of heat-sinking a component to the PCB, but your question about the Ferric Chloride nulls that assumption. I'm confused on what exactly you are speaking of. :?:
As far as the green stuff, the most common name is "Solder mask". It is basically a coating that keeps the copper and solder from corrosion, tarnish, accidental shorting (in most cases) etc. Most electronics suppliers will carry this Solder mask, or a version of it.