This paper reports a unified synthesis taxonomy in design of three-dimensional (3D) molecular integrated circuits (MICs). TheseMICs, fabricated utilizing bottom-up molecular fabrication technologies, are designed as aggregated neuronal hypercells ([unk]hypercell). Each[unk]hypercell is implemented using molecular gates (Mgates) which composed from multi-terminal molecular electronic devices that exhibit and operate due to quantum phenomena. The intelligent library of[unk]hypercell aggregates,,[unk]hypercells,Mgates, molecular devices and data-structure primitives can be developed and utilized. To address complexity and technology dependence, this paper documents innovative methods in design, optimization, evaluation and verification of 3DMICs. The logic design ofMICs is accomplished by using a novel technology-centric concept based on the use of[unk]hypercells and linear decision diagrams. We initiate the developments of a 3D super-large-scale integration (3DSLSI) design concept. This paper reports a proof-of-concept CAD design tools illustrating and verifying the results for combinationalMICs.