An improved, lower cost method of processing substrates, such as to create solar cells is disclosed. The doped regions are created on the substrate, using a mask or without the use of lithography or masks. After the implantation is complete, visual recognition is used to determine the exact region that was implanted. This information can then be used by subsequent process steps to maintain this alignment. This information can also be fed back to the ion implantation equipment to modify the implant parameters. These techniques can also be used in other ion implanter applications.