A method is disclosed that includes forming at least one substrate alignment mark and at least one lithography alignment mark in a substrate; forming a seed layer on the substrate; and forming a guide pattern and at least one guide pattern alignment mark in the seed layer, where the at least one guide pattern alignment mark is formed over the at least one substrate alignment mark. The method further includes determining an alignment error of the at least one guide pattern alignment mark relative to the at least one substrate alignment mark; and patterning features on at least one region of the substrate, where the features are positioned on the substrate based on the at least one lithography alignment mark and the alignment error.