AtMol will establish comprehensive process flow for fabricating a molecular chip, i.e. a molecular processing unit comprising a single molecule connected to external mesoscopic electrodes with atomic scale precision and preserving the integrity of the gates down to the atomic level after the encapsulation. Logic functions will be incorporated in a single molecule gate, or performed by a single surface atomic scale circuit, via either a quantum Hamiltonian or a semi-classical design approach. AtMol will explore and demonstrate how the combination of classical and quantum information inside the same atomic scale circuit increases the computing power of the final logic circuit. Atomic scale logic gates will be constructed using atom-by-atom manipulation, on-surface chemistry, and unique UHV transfer printing technology. The AtMol research programme necessitates the state-of-the-art UHV atomic scale interconnection machines comprising, within one integrated UHV system, a surface preparation chamber, a UHV transfer printing device, an LT-UHV-STM (or a UHV-NC-AFM) for atomic scale construction, a FIM atomic scale tip apex fabrication device and a multi-probe system with its companion SEM or optical navigation microscope. Only three of these systems exist worldwide and they are each housed within the laboratories members of the AtMol consortium. These systems will be used to interconnect molecular logic gates one-by-one in a planar atomic scale multi-pad approach on the top, atomically reconstructed, surface of the wafer. For this molecular chip, the back face of the wafer will incorporate nano-to-micro-scale interconnections using nanofabricated vias which pass through the substrate to the top face. The hybrid micro-nano back interconnect approach to be developed in the AtMol project will enable the full packaging of the molecular chip preserving the surface atomic scale precision of the gates.