In one aspect of the inventive method, a tunnel insulating film, a first conductive layer, and an isolation mask pattern are formed over a semiconductor substrate. The first conductive layer and the tunnel insulating film are patterned along the isolation mask pattern. A trench is formed in the semiconductor substrate. The trench is gap filled with a first insulating film. A polishing process is performed in order to expose the first conductive layer. A height of the first insulating film is lowered. The first conductive layer on the first insulating film is gap-filled with a second insulating film.