Free to pursue his own goals, he entered the workshops of Marie-Joseph Peyre, and attended classes at the Académie royale d'architecture.
Later that year, he left for a five-year stay at the Académie de France à Rome; in the Palazzo Mancini.
In 1791, when it was proposed that the Church of Sainte-Geneviève, recently completed, be transformed into what is now called the Panthéon, he expressed his strong opposition.
Vaudoyer joined with Julien-David Le Roy, a former Professor there, to open an independent school of architecture.
He was named a member of the Académie des Beaux-Arts in 1823, where he took Seat #2 for architecture ; succeeding Antoine-François Peyre (deceased).