An improved, lower cost method of processing substrates, such as to create solar cells is disclosed. In addition, a modified substrate carrier is disclosed. The carriers typically used to carry the substrates are modified so as to serve as shadow masks for a patterned implant. In some embodiments, various patterns can be created using the carriers such that different process steps can be performed on the substrate by changing the carrier or the position with the carrier. In addition, since the alignment of the substrate to the carrier is critical, the carrier may contain alignment features to insure that the substrate is positioned properly on the carrier. In some embodiments, gravity is used to hold the substrate on the carrier, and therefore, the ions are directed so that the ion beam travels upward toward the bottom side of the carrier.