A method for manufacturing a semiconductor device and a device manufactured by the same are provided. According to the embodiment, a substrate having at least a first area with a plurality of first gates and a second area with a plurality of second gates is provided, wherein the adjacent first gates and the adjacent second gates separated by an insulation, and a top surface of the insulation has a plurality of recesses. Then, a capping layer is formed over the first gate, the second gates and the insulation, and filling the recesses. The capping layer is removed until reaching the top surface of the insulation, thereby forming the insulating depositions filling up the recesses, wherein the upper surfaces of the insulating deposition are substantially aligned with the top surface of the insulation.