A method of processing a substrate includes mounting a substrate on a concave mounting surface of a mounting table and deforming a surface of the substrate into a concave shape; detecting, by a height sensor, a height of the surface of the substrate in a vertical direction; determining positions of a plurality of first focus points based on height data of the surface of the substrate, detected by the height sensor; and forming a first modification layer in the substrate by irradiating the plurality of first focus points with a laser beam.