Despite the locations - France and continental Europe - it was filmed almost entirely in the UK and a bit in Malta.
Notre Dame de Paris
In movie
Scene where Napoleon conducts the coronation of himself as Emperor of France.
Real
Scene was shot actually filmed the scene not in Paris, but in the main hall of Lincoln Cathedral in Lincoln, UK.
Lincoln
Lincoln Cathedral
Refectory
In movie
Scene where Napoleon is talking to Josephine.
Real
Scene was shot in the Great Marble Hall, Blenheim Palace.
Woodstock
Blenheim Palace