1. A method of manufacturing a silicon carbide semiconductor device, comprising the steps of: preparing a silicon carbide substrate having a main surface angled off relative to a {0001} plane; forming a protruding first alignment mark on said main surface of said silicon carbide substrate; forming a second alignment mark on said first alignment mark by forming a silicon carbide epitaxial layer on said first alignment mark; and performing alignment of said silicon carbide substrate using said second alignment mark, said first alignment mark including a first region and a second region, said second region being in contact with said first region and extending from said first region in an off direction in which a <0001> direction is projected onto said main surface, said first region including a short side along a direction parallel to said off direction, and a long side along a direction perpendicular to said off direction within said main surface, said second alignment mark including a first portion formed on said first region and a second portion formed on said second region, said step of performing alignment including the step of capturing an image of said first portion while not including said second portion, and recognizing an edge of said first portion based on said image.