A system and method for patterning of a substrate at sub-micron length scales using interference lithography that includes a substrate; a chuck that promotes substrate motion; at least two EM beams; a beam phase controller, wherein the phase controller modifies phases of the EM beams with respect to each other creating an interference pattern; a displacement sensor that measures the substrate displacement; and a feedback control mechanism configured to monitor and synchronize the substrate motion with the interference pattern using the beam phase controller and the displacement sensor.