A monolithic three dimensional semiconductor device structure includes a first layer including a first occurrence of a first reference mark at a first location, and a second layer including a second occurrence of the first reference mark at a second location, wherein the second location is substantially directly above the first location. The device structure also includes an intermediate layer between the first layer and the second layer, the intermediate layer including a blocking structure, wherein the blocking structure is vertically interposed between the first occurrence of the first reference mark and the second occurrence of the first reference mark. Other aspects are also described.