A system and method are disclosed for aligning substrates during successive process steps, such as ion implantation steps, is disclosed. Implanted regions are created on a substrate. After implantation, an image is obtained of the implanted regions, and a fiducial is provided on the substrate in known relation to at least one of the implanted regions. A thermal anneal process is performed on the substrate such that the implanted regions are no longer visible but the fiducial remains visible. The position of the fiducial may be used in downstream process steps to properly align pattern masks over the implanted regions. The fiducial also may be applied to the substrate before any ion implanting of the substrate is performed. The position of the fiducial with respect to an edge or a corner of the substrate may be used for aligning during downstream process steps. Other embodiments are described and claimed.