Since you have a MacBook pro you could try to just open the case. You don't necessarily need to rip out the motherboard, but check for loose screws or detached parts. Maybe screwing the case back on could fix the problem.
I have a similar issue with my 4 months old macBook Air. It creaks and makes snapping noises in the bottom case when i lift it or in any other way slightly bend it.
I took it to apple and they "had never heard of the problem" and wanted to charge me just to open the case and put it back on again to see if that was the problem. They said it was not covered by the guarantee either. I decided that it was a very expensive noise and took it back home without fixing it. The MacBook Pro should be easier to open, the one i have from 2012 has standard screws instead of apple ones.