A method of manufacturing a flash memory cell in which an ion implantation process is performed before a cleaning process for etching a protrusion of a trench insulating film to a nipple shape. As a result, the etch rate at a portion except for portions in which a moat will occur along the trench insulating film is increased. Therefore, generation of the moat in the trench insulating film can be prevented and spacing of the floating gate can be optimized.