Abstract: A wafer alignment system aligns a wafer by checking the alignment marks formed on the back surface of the wafer. A number of guiding rays are used to determine the corresponding alignment mark on the back of the wafer to ensure that the wafer is properly aligned. The alignment system of the invention also includes a wafer stage and a fixed base, wherein the wafer stage and the fixed base contains a number of apertures that allow the guiding rays to pass through and strike on the alignment marks on the wafer.