A method of processing a substrate which enables a surface damaged layer and polishing remnants on the surface of an insulating film to be removed, and enable the amount removed of the surface damaged layer and polishing remnants to be controlled easily. An insulating film on a substrate, which has been revealed by chemical mechanical polishing, is exposed to an atmosphere of a mixed gas containing ammonia and hydrogen fluoride under a predetermined pressure. The insulating film which has been exposed to the atmosphere of the mixed gas is heated to a predetermined temperature.