A method comprises the steps of forming a damaged layer on a silicon substrate by subjecting the silicon substrate to a plasma treatment, forming a silicon oxide layer by exposing the surface of the damaged layer to an oxygen plasma to oxidize the surface of the silicon substrate including the damaged layer and selectively eliminating the silicon oxide layer under a condition of a high selective ratio to the silicon, in which the film thickness of the silicon oxide layer is controlled by controlling an ion energy of the oxygen plasma and exposure time of the surface of the damaged layer to the oxygen plasma in accordance with the film thickness of the damaged layer.