The point of the philosopher's stone was to purify baser metals and turn them to gold, that is, the "parts" of the metals that were impure would be removed:
Matter transmutation, the old goal of alchemy, enjoyed a moment in the sun in the 20th century when physicists were able to convert platinum atoms into gold atoms via a nuclear reaction. However, the new gold atoms, being unstable isotopes, lasted for under five seconds before they broke apart. More recently, reports of table-top element transmutation—by means of electrolysis or sonic cavitation—were the pivot of the cold fusion controversy of 1989. None of those claims have yet been reliably duplicated. (Wikipedia, Alchemy.)However, gold is relatively useless. What is wanted is energy. And we have a philosopher's stone for that--nuclear reactions, which transmute otherwise useless material into energy. There are prices to be paid for the transmutation when one is talking about nuclear energy...but rarely if you're talking about the philosopher's stone.
...I was trying to figure out a story for that when I realized there already was one: Indiana Jones and the Raiders of the Lost Ark. Beaten to the punchline again.