In this method of manufacturing a semiconductor device, the remaining layer of an etching mask layer remains in a predetermined thickness when the stamping face of a nano-stamper is pressed on the surface of the etching mask layer. Therefore, the remaining layer of the etching mask layer functions as a cushion so that the stress added to the nano-stamper and the semiconductor substrate is reduced. Accordingly, the crystal defect that might otherwise be introduced in the semiconductor substrate in pressing the nano-stamper on the semiconductor substrate can be restrained, resulting in suppression of the degradation of optical characteristics of the semiconductor device. Also, since the nano-stamper can be prevented from being damaged, extra steps such as the replacement of the nano-stamper can be avoided.