A silicon carbide substrate is prepared which has a main surface covered with a silicon dioxide layer. In the silicon dioxide layer, an opening is formed by etching. In the opening, a residue resulting from the etching is on the silicon carbide substrate. The residue is removed by plasma etching in which only an inert gas is introduced. After removing the residue, under heating, a reactive gas is supplied to the silicon carbide substrate covered with the silicon dioxide layer having the opening formed therein. In this way, a trench is formed in the main surface of the silicon carbide substrate.