A method of manufacturing a semiconductor device includes forming an isolation region defining an active region in a semiconductor substrate, forming a first insulating film over the semiconductor substrate, forming a second insulating film having etching properties different from those of the first insulating film over the first insulating film, selectively removing the second insulating film from a first region over the active region and the isolation region by dry etching using a fluorocarbon-based etching gas, removing a residual film formed by the dry etching over the first insulating film by exposure in an atmosphere containing oxygen, and selectively removing the first insulating film from the first region by wet etching.