After a plurality of trenches is formed in an SOI substrate, a side surface of the insulating layer is retreated from a side surface of the semiconductor layer and a side surface of the semiconductor substrate. Next, the side surface of the insulating layer is covered with an organic film and also the side surface of the semiconductor layer is exposed from the organic film by performing an anisotropic etching process to the organic film embedded into an inside of each of the plurality of trenches. Next, each of the side surface of the semiconductor layer and the side surface of the semiconductor substrate is approached to the side surface of the insulating layer by performing an isotropic etching process. Further, after the organic film is removed, an oxidation treatment is performed to each of the side surface of the semiconductor layer and the side surface of the semiconductor substrate.