The authors develop a step-and-align interference lithography system to fabricate large-area periodic submicron structures by stitching the unit exposure area step-by-step. A metal mask with a square transparent window in the center is used to intercept the quasi-flat-top region of the expanded Gaussian beam, and thus it serves as a beamshaper to approximate the ideal unit beam that has uniform intensity and spatial coherence. Two-dimensional precision dual-actuator motion stages could provide travel distance for full wafer exposure with 2 nm high precision positioning capability for stitching the submicron patterns. The gratings with period of 700 nm are successfully stitched along two directions on 100 mm diameter wafers.