A method for manufacturing a semiconductor device includes forming a plurality of trenches for element isolation and a plurality of trenches for alignment mark on a substrate. The substrate has an active region. The method also includes laminating an oxide film on the substrate and over both of the trenches. The method also includes etching the oxide film using a resist mask that masks the element isolation trenches, so that the oxide film laminated in the active region and the oxide film laminated in the alignment mark trenches are removed. The method also includes polishing a surface of the substrate to planarize or smooth the surface of the substrate. Accordingly, those portions of the oxide film which project from the substrate surface are eliminated and the oxide film remains only inside the element isolation trenches. This divides the active region into a plurality of individual active regions for the respective semiconductor elements. The method also includes positioning the resist mask using the alignment mark trenches. The resist mask is used to fabricate the semiconductor elements in the active regions of the substrate.