Abstract: A multi-level registration control system for a photolithography process includes a photolithography device that prints first, second and third layers on a wafer. A first overlay mark defines overlay errors in a first direction between the first and third layer. The first overlay mark also defines overlay errors between the second and third layers. An overlay measurement device measures the overlay errors and generates an overlay signal. A feedback controller is connected to the overlay measurement device and the photolithography device. The feedback controller receives the overlay error signal and generates and transmits an alignment correction signal to the photolithography device. The first overlay mark is a box-in-box overlay mark or a frame-in-frame overlay mark. By providing a single overlay mark to align three layers, the multi-layer overlay control system reduces scribe grid area and saves useful silicone surface area.