There is method of processing a substrate comprising: (a) providing the substrate with a first base containing no oxygen, a second base containing oxygen, and a third base containing no oxygen and no nitrogen on its surface, wherein a protective film is formed on a surface of the third base; (b) modifying a surface of the second base to be fluorine-terminated by supplying a fluorine-containing gas to the substrate in a state where the protective film is formed on the surface of the third base; and (c) forming a film on a surface of the first base by supplying a film-forming gas to the substrate in a state where the surface of the second base is modified.