According to one embodiment, a method is disclosed for manufacturing a semiconductor device. The method can include forming a stacked layer in a memory cell region and a mark region, forming a first mask layer above the stacked layer, and forming a second mask layer above the first mask layer; forming the second mask layer into first mask pattern features and forming a first alignment mark pattern feature; forming second mask pattern features and then removing the first mask pattern features; opening part of the second mask pattern features and forming a third mask layer having an opening; removing part of the second mask pattern features; removing the third mask layer; forming a fourth mask layer; etching the first mask layer; removing the fourth mask layer and then removing the second mask pattern features; and etching the stacked layer.