A method of verifying an integrated circuit stack includes adding a first dummy layer to a first contact pad of a circuit, wherein a location of the first dummy layer is determined based on a location of a second contact pad of a connecting substrate. The method further includes converting the first dummy layer location to the connecting substrate. The method further includes adjusting the first dummy layer location in the circuit in response to a determination that the first dummy layer location is misaligned with the second contact pad. The method further includes performing a first layout versus schematic (LVS) check of the connecting substrate including the first dummy layer in response to a determination that the first dummy layer is aligned with the second contact pad.