Two pieces of semiconductor wafers 10.sub.1 and 10.sub.2 to be stacked and fused together are secured to wafer holders 20.sub.1 and 20.sub.2 respectively, and are then integrally held at a wafer hold unit 2. Rough position alignment is first applied to these semiconductor wafers 10.sub.1 and 10.sub.2 while supplying infrared light thereto from an infrared light source 30 of an infrared light system 3 for detection of a resultant lattice image at a detection unit 5. Then, fine position, alignment is performed while supplying laser light from an laser light source 40 of a laser light system 4 for detection of a resultant diffraction image at the detection unit 5. Thus, in the manufacture of a semiconductor-device having its crystal structure with three-dimensional periodical refractive index distribution employing precision multilayer stack methods by using a wafer fusion, a method and apparatus for manufacturing the semiconductor device is realized which is capable of achieving precise position alignment between lattice layers stacked over each other with reduced complexity in position alignment thereof.