Ion bombardment during inductively coupled plasma reactive-ion etching and ion-implantation introduces irreparable crystalline damage to gallium nitride (GaN) power devices, leading to early breakdown and high leakage current. To circumvent this, a bi-layer selective area growth mask was engineered to grow up to 3.0 µm thick epitaxy of GaN using plasma-assisted molecular beam epitaxy as an ion-damage-free alternative to standard epitaxial processing routes. The masks and regrown architectures are characterized via SEM, conductive-atomic force microscopy (AFM), x-ray photo electron spectroscopy, Raman, and cathodoluminescence. Mask deposition conditions were varied to modulate and minimize the stress induced during thermal cycling. The resulting mesas exhibit low leakage, attributed to naturally terminated sidewalls as measured by an innovative perpendicular AFM measurement of the regrown sidewall. The regrown sidewall exhibited RMS (root mean square) roughness of 1.50 (±0.34) nm and defect density of 1.36 × 106 (±1.11 × 106) cm−2. This work provides a method to eliminate defect-inducing steps from GaN vertical epitaxial processing and stands to enhance GaN as a material platform for high-efficiency power devices.