Group III-Nitride three-dimensional structures have gained substantial interest for application in optoelectronic, energy, and sensor devices with non-planar geometries [1-4]. The benefits of 3D structures, such as GaN-based nano-/micro-rods, compared to planar films include large surface area, high structural quality, non-polar-surface utilization, small footprint, mechanical flexibility, and enhanced light absorption/extraction efficiency. To advance the technology of non-planar III-Nitride semiconductors, it is necessary to optimize and scale up the fabrication of such structures with controlled geometries and desired electronic and optical properties. Here, we report the fabrication of wafer-scale periodic arrays of vertically aligned GaN core-shell micropillars using a combination of top-down etch and epitaxial overgrowth.The two-step process consists of inductively coupled plasma (ICP) etching of lithographically patterned GaN-on-Si substrate to produce an array of micropillars followed by selective growth of GaN shells over these pillars using Hydride Vapor Phase Epitaxy (HVPE). The most significant aspect of the study is the demonstration of the sidewall facet control in the shells, ranging from truncated hexagonal pyramids with the (1-101) semi-polar sidewalls to hexagonal prisms with the (1-100) non-polar sidewalls, by employing a post-ICP wet chemical etch and by tuning the HVPE growth temperature. Optimization of both ICP etching and epitaxial overgrowth reduced dislocation density in the GaN shells, thus enhancing the transport and optical characteristics of these device platforms. Photo- and cathodoluminescence showed a substantial reduction of parasitic yellow luminescence as well as strain-relaxation in the core-shell structures, supported by Raman scattering, electron-backscatter-diffraction (EBSD), and X-ray-diffraction measurements. Transmission electron microscopy revealed improved crystal quality with reduced dislocation density in the epitaxially grown shells. This work demonstrates the feasibility of selective epitaxy on micro/nano-engineered 3D templates for realizing high-quality GaN-on-Si devices such as LEDs and p-i-n photodetectors.