A method of manufacturing a semiconductor device includes forming a lower film including a cell region and a peripheral circuit region, forming a first sacrificial film on the lower film, the first sacrificial film having trenches in the cell region, forming a second sacrificial pattern on the first sacrificial film, the second sacrificial pattern having line-shaped patterns spaced apart from each other and crossing the trenches in the cell region, and the second sacrificial pattern covering a top surface of the first sacrificial film in the peripheral circuit region, and patterning the first sacrificial film to form upper holes in portions of the trenches exposed by the second sacrificial pattern.