A system for aligning a first and second pattern based on alignment structures is disclosed. The system comprises a first substrate including the first alignment structure. The alignment structure has a different magnitude of the electrical characteristic than the substrate. The system also includes an electrical probe and a controller for controlling the relative position of the probe with respect to the substrate to measure the electrical characteristic at a plurality of positions proximate the substrate. The measured electrical characteristics are used to identify the location of the alignment structure by identifying a difference between the measured electrical characteristic at pairs of the plurality of positions. A controller identifies the location of a second alignment structure formed on a second substrate. A registration mechanism aligns the two substrates using the identified locations of the first and second alignment structures.