A substrate including an insulating layer, a semiconductor layer, and an insulating film stacked on a semiconductor substrate and having a trench filled with an element isolation portion is provided. After removal of the insulating film from a bulk region by a first dry etching, the semiconductor layer is removed from the bulk region by a second dry etching. Then, the insulating film in an SOI region and the insulating layer in the bulk region are removed. A gas containing a fluorocarbon gas is used for first dry etching. The etching thickness of the element isolation portion by a first dry etching is at least equal to the sum of the thicknesses of the insulating film just before starting the first dry etching and the semiconductor layer just before starting the first dry etching. After first dry etching and before second dry etching, oxygen plasma treatment is performed.