A technique for preventing a decrease in alignment accuracy during a photolithography process is provided. A substrate (1) is prepared, in the surface (80) of which trenches (7) for use as alignment marks and trenches (17, 27) each forming an element isolation structure are formed and on the surface (80) of which a polysilicon film (3) is formed, avoiding the trenches (7, 17, 27). The trenches (7, 17, 27) are filled with an insulation film (30). The insulation film (30) is then selectively etched to partially remove the insulation film (30) in the trenches (7) and to leave the insulation film (30) on side and bottom surfaces (81, 82) of the trenches (7). Using the insulation film (30) in the trenches (7) as a protective film, the polysilicon film (3) is selectively etched. The use of the insulation film (30) in the trenches (7) as a protective film prevents the substrate (1) from being etched and thereby prevents the shape of the trenches (7) from being changed. This results in prevention of a decrease in alignment accuracy during a photolithography process.