A method of manufacturing a semiconductor device is disclosed which comprises forming a gate structure on a major surface of a semiconductor substrate with a gate insulating film interposed therebetween, forming a first insulating film to cover top and side surfaces of the gate structure and the major surface of the semiconductor substrate, reforming portions of the first insulating film which cover the top surface of the gate structure and the major surface of the semiconductor substrate by an anisotropic plasma process using a gas not containing fluorine, and removing the reformed portions of the first insulating film.