A manufacturing method for manufacturing a super-junction semiconductor device forms an oxide film and a nitride film on an n-type epitaxial layer exhibiting high resistance on an n-type semiconductor substrate exhibiting low resistance. The portion of the nitride film in the scribe region is left unremoved by patterning and an alignment marker is opened through the nitride film. After opening a trench pattern in the oxide film, trenches having a high aspect ratio are formed. The portion of the oxide film outside the scribe region is removed and a p-type epitaxial layer is buried in the trenches. The overgrown p-type epitaxial layer is polished with reference to the nitride film, the polished surface is finished by etching, and the n-type epitaxial layer surface is exposed.