Certain aspects relate to systems and techniques for submicron alignment in wafer optics. One disclosed method of alignment between wafers to produce an integrated lens stack employs a beam splitter (that is, a 50% transparent mirror) that reflects the alignment mark of the top wafer when the microscope objective is focused on the alignment mark of the bottom wafer. Another disclosed method of alignment between wafers to produce an integrated lens stack implements complementary patterns that can produce a Moiré effect when misaligned in order to aid in visually determining proper alignment between the wafers. In some embodiments, the methods can be combined to increase precision.