An array of contact pads on a semiconductor structure has a pitch less than twice an overlay tolerance of a bonding process employed to vertically stack semiconductor structures. A set of contact pads within the area of overlay variation for a matching contact pin may be electrically connected to an array of programmable contacts such that one programmable contact is connected to each contact pad within the area of overlay variation. One contact pad may be provided with a plurality of programmable contacts. The variability of contacts between contact pins and contact pads is accommodated by connecting or disconnecting programmable contacts after the stacking of semiconductor structures. Since the pitch of the array of contact pins may be less than twice the overlay variation of the bonding process, a high density of interconnections is provided in the vertically stacked structure.