A method of manufacturing a semiconductor device includes forming a first pattern structure having a first opening and a second pattern structure having a second opening on a substrate, forming a gap fill layer in the second opening, forming fences and contact structures in the first opening, removing the gap fill layer in the second opening, forming an upper conductive layer to cover the first and second pattern structures, the fences, and the contact structures, forming a mask pattern based on a photolithography process using the second pattern structure covered by the upper conductive layer as an align mark, and etching the upper conductive layer using the mask pattern to form upper conductive patterns. A width of the second opening is larger than a width of a first opening. A thickness of the upper conductive layer is smaller than a depth of the second opening.