Philosopher's Stone or Philosophi Lapis

This is considered by many to have been a substance that the Alchemists searched for that could turn Base Metal into Gold.  The search for this substance was often called Alchemy.

It was also considered to be an elixir that could make people younger, or perhaps better.

Can Freemasonry be considered as the Philosopher's Stone, or Philosophi Lapis, since Freemasonry attempts to make good men better?

The search for the Philosopher's Stone was often done in secrecy.  Secrecy was needed since most people could not understand the concept. The Catholic Church especially did not like people who studied Science and had many Scientists Burned at the Stake as heretics or blasphemers.  This led to a large number of Secret Societies in Europe.

It was believed that the search for the Philosopher's Stone could only be undertaken by the adepts.

The use of symbols was common in Alchemy, as it is in Freemasonry today.  Symbolism is also used by a lot of Religions, including Christianity, to get across their point.