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Current computational electronics are on a course potentially to overtake already large sectors such as transportation in energy consumption. Hopefully, a solution can be found that both maintains quality of life and vastly reduces energy consumption. One particular solution is a class of computing called Quantum Computing. While there are many architectures being pursued at the moment, we believe that dopant based qubits can be a fundamental element of the Quantum Computer solution. Currently, progress is being made in carefully placing dopant qubits in a single 2D plane inside silicon crystals, but there is an eventual problem in accessing these qubits. Based on a 3 layer structure proposed by Charles Hill, we in Phase I are taking steps to produce the first two layers of such prototype devices through studies in materials science, solid state physics, and Atomically Precise Lithography. This will be done by producing a bottom control layer using methods already known, then reproducing another atomically flat surface after growing more silicon crystal a few tens of nanometers above the first surface. Success with this will enable 3D device architectures so that the number of wires scales with the square root of the number of qubits instead of scaling with the number of qubits. Success in Phases I and II will lead to several potential commercial applications. Potentially the largest impact will be to drive investment into 2D systems of qubits using 3D architectures. Another indirect potential commercial application would be demonstration of the ability to make 3D metamaterials where each layer of material can be individually designed. The metrology capabilities could advance new industries such as semiconductor probing for QA/QC. With the versatility of 3D fabrication within a single crystal, this could drive yet undiscovered research and development.