In a multi-mask alignment system and method, a carrier frame is provided having a number of apertures therethrough. A number of shadow mask-frame combinations are also provided. Each shadow mask-frame combination includes a first set of alignment features and each shadow mask-frame combination is positioned on a first side of the carrier with the frame supporting the shadow mask in alignment with one of the apertures. An alignment system is provided and a control system including a programmed controller is also provided. Under the control of the controller, the alignment system is caused to adjust the position of each shadow mask-frame combination with respect to the carrier based on positions of the first set of alignment features determined by the controller.