A method of manufacturing a semiconductor device includes forming a first insulating film having a first thickness over a main surface of a semiconductor substrate and then forming a second insulating film having a second thickness larger than the first thickness over the first insulating film, sequentially processing the second insulating film, the first insulating film, and the semiconductor substrate to form a plurality of trenches and to form a plurality of projecting portions which include portions of the semiconductor substrate extending in a first direction along the main surface of the semiconductor substrate and are spaced apart from each other in a second direction orthogonal to the first direction along the main surface of the semiconductor substrate, and depositing a third insulating film over the main surface of the semiconductor substrate such that the third insulating film is embedded in the trenches.