An apparatus, program product and method facilitate the design of a multi-layer circuit arrangement incorporating a universal, standardized inter-layer interconnect in a multi-layer semiconductor stack to facilitate interconnection and communication between functional units disposed on a stack of semiconductor dies. Each circuit layer in the multi-layer semiconductor stack is required to include an inter-layer interface region that is disposed at substantially the same topographic location such that when the semiconductor dies upon which such circuit layers are disposed are arranged together in a stack, electrical conductors disposed within each semiconductor die are aligned with one another to provide an inter-layer bus that is oriented vertically, or transversely, with respect to the individual circuit layers.