Three-dimensional (3D) nano-structures are vital for emerging technologies such as photonics, sensors, fuel cells, catalyst supports, and data storage. The Proximity-field nanoPatterning1 method generates complex 3D nanostructures using a single exposure through an elastomeric "phase mask" patterned in x, y, and z, and a single development cycle. We developed a model that predicts the phase mask required to generate a specific desired nanostructure. We have compared this inverse model with experimental 3D structures to test the validity of the simulation. We have transferred the PnP fabrication process to a class-10 commercial cleanroom and scaled-up the processed area to >2000mm2, tested photopolymer additives designed to reduce resist shrinkage, incorporated atomic layer deposition (ALD) to coat the 3D patterned resist with metals/metal-oxides improve structure robustness, and generated quasi-crystal patterned 3D nanostructures.