Methods and apparatuses for manufacturing self-aligned integrated back contact heterojunction solar cells are provided. In some embodiments, systems for forming a solar cell on a substrate are provided, the systems comprising: a master shadow mask positioned adjacent to the substrate on a first side of the master shadow mask; a first blocking mask placed adjacent to a second side of the master shadow mask; and a deposition machine that deposits material on the substrate through holes in the master shadow mask and the first blocking mask.