A method of manufacturing bonded substrate structures. The method includes providing a first substrate comprising a first surface region and processing the first surface region to form a first pattern region using a first photolithographic stepper characterized by a first tolerance criteria for alignment. The method also includes providing a second substrate comprising a second surface region and processing the second surface region through at least one masking process to form a second pattern region using a second photolithographic stepper characterized by a second tolerance criteria for alignment. Further, the method includes determining a masking process having a third tolerance criteria for alignment, the third tolerance criteria allowing for a change from the second to the first photographic stepper, processing the second substrate for at least the determined masking process using the first photolithographic stepper, and joining the first substrate to the second substrate to form a composite substrate structure.