In a method of processing a substrate, in a second step, only some of a plurality of altered portions are exposed from an opening portion of a mask, and the remaining portions are not exposed. In this case, at the time of etching in a third step, an etching rate may be made different between the altered portions exposed from the opening portion of the mask and the altered portions which are not exposed. Accordingly, it becomes easier to obtain a desired processed shape by adjusting the altered portions exposed from the opening portion of the mask and the altered portions which are not exposed.