On his return Thomas Vaughan tarried a short time in France, where he conceived the project of organising Freemasonry as it exists at the present day, and there also it occurred to him that the guilds of the Compagnage might serve him for raw material.

When, however, he returned to England, he concluded that the honorary or Accepted Masons, received by the Masonic guilds of England, were better suited to his purpose.

Some of these were already Rosicrucians, and among them he set to work.

In the year 1644 he presided over a Rosicrucian assembly at which Ashmole was present.

At this time also Oliver Cromwell is said to have been an accepted Mason, and it was by his intervention that, a year later, Thomas Vaughan was substituted for the headsman at the execution of Archbishop Laud, for the object already described.