Deep via trenches and deep marker trenches are formed in a bulk substrate and filled with a conductive material to form deep conductive vias and deep marker vias. At least one first semiconductor device is formed on the first surface of the bulk substrate. A disposable dielectric capping layer and a disposable material layer are formed over the first surface of the bulk substrate. The second surface, located on the opposite side of the first surface, of the bulk substrate is polished to expose and planarize the deep conductive vias and deep marker vias, which become through-substrate vias and through-substrate alignment markers, respectively. At least one second semiconductor device and second metal interconnect structures are formed on the second surface of the bulk substrate. The disposable material layer and the disposable dielectric capping layer are removed and first metal interconnect structures are formed on the first surface.