A semiconductor device comprising: a first single crystal silicon layer comprising first transistors, first alignment mark, and at least one metal layer overlying said first single crystal silicon layer, wherein said at least one metal layer comprises copper or aluminum more than other materials; a second layer overlying said at least one metal layer, said second layer comprising second transistors, second alignment mark, and a through via through said second layer, wherein said through via is a part of a connection path between said first transistors and said second transistors, wherein alignment of said through via is based on said first alignment mark and said second alignment mark and effected by a distance between said first alignment mark and said second alignment mark.