A semiconductor device manufacturing method includes preparing a wafer having projections formed on a substrate. The projections project upward from a surface of the substrate and have a height measured from the surface of the substrate. The method further includes determining an interval distribution representing a distribution of intervals between neighboring projections and calculating an implantation angle based on the height and the interval distribution. The implantation angle is an angle between a normal direction of the substrate and an implantation direction. The method also includes implanting ions at the calculated implantation angle.