The present invention includes a method and system for forming a semiconductor device. Varying embodiments generate 2 dimensional alignment features in a device by implementing a 3-dimensional pattern into an underlying device substrate. Accordingly, alignments between successive device patterning steps can be determined regardless of the dilations or contractions that can take place during the device fabrication process. A first aspect of the present invention is a method for forming a semiconductor device. The method includes forming a 3-dimensional pattern in a substrate and depositing at least one material over the substrate in accordance with desired characteristics of the semiconductor device.