Disclosed is a method and a system for forming alignment marks on a transparent substrate. A light reflective layer is deposited over an optically transparent substrate of a wafer. A region is defined around an alignment mark on the optically transparent substrate. The light reflective layer is removed from a substantial portion of the transparent substrate excluding the region. In addition, a micro electro-mechanical systems device is disclosed. The device comprises an optically transparent substrate, at least one optically partially transparent alignment mark on the optically transparent substrate, and a plurality of reflective elements or imaging pixels attached to the optically transparent substrate.