A method of manufacturing a semiconductor device includes selecting a diffraction based focus (DBF) mark that is unaffected by a pattern of a lower layer; manufacturing a mask including a mark pattern for forming the DBF mark; forming the DBF mark in a cell region of a wafer by using the mask; measuring the DBF mark and monitoring defocus; correcting the defocus on the basis of a result of the monitoring; and forming a pattern in the cell region of the wafer, after correcting the defocus.