In one embodiment, a mask set for use in fabricating thin film tunneling devices includes a first photomask configured to form bottom electrodes of the devices, the first photomask comprising a first alignment mark including multiple corner markers, and a second photomask configured to form a continuous top layer of the devices, the second photomask comprising a second alignment mark including a corner marker configured to be aligned with one of the corner markers of the first photomask, wherein a degree of overlap between the bottom electrodes and the continuous top layer depends upon the corner marker of the first photomask with which the corner marker of the second photomask aligns.