In one embodiment, a method of manufacturing a semiconductor device includes forming a first film on a substrate. The method further includes performing a first process of forming a concave portion in the first film and forming a second film on a surface of the first film that is exposed in the concave portion by using a first gas containing a carbon element and a fluorine element. The method further includes performing a second process of exposing the second film to a second gas containing a hydrogen element or a fluid generated from the second gas.