A method for aligning multiple substrates. The method includes providing a handle substrate, providing a spacer substrate, and forming a plurality of first alignment marks on a first surface of the handle substrate. The method also includes forming a plurality of self-limiting alignment marks on a first surface of the spacer substrate and forming a plurality of openings in the spacer substrate, each of the plurality of openings surrounded by standoff regions. The method further includes aligning the first surface of the handle substrate and the first surface of the spacer substrate using the first alignment marks and the self-limiting alignment marks and bonding the handle substrate to the spacer substrate to form a composite substrate structure. In a specific embodiment, the plurality of self-limiting alignment marks and the plurality of openings are formed using an anisotropic wet etching process that preferentially etches the spacer substrate.