A method of manufacturing a semiconductor device includes: providing a substrate, forming a first opening, forming a first insulating layer, forming a second opening, embedding a conductive layer, forming a protective layer, and performing CMP. The substrate includes a semiconductor substrate and a semiconducting layer. The conductive layer is embedded in the second opening so that a gap along a thickness direction of the semiconducting layer is formed. The protective layer is formed in the second opening on at least a portion of a surfaces of the conductive layer. In the CMP step, a portion of the conductive layers formed outside the second opening is removed.