GaN substrates and epilayers were evaluated using X-ray topography and high-resolution X-ray diffraction (HRXRD) techniques, which provide quantitative maps of strain and tilt and, in conjunction with ray-tracing simulations, provide the distribution of extended defects. X-ray topography shows ammonothermal-grown GaN substrates have the lowest dislocation densities, while hydride vapor phase epitaxy- (HVPE) grown substrates contain high dislocation densities. Patterned HVPE-grown substrates have a heterogeneous distribution of dislocations with large areas containing low densities. Substrates and epilayers subject to selective area doping processes for Mg p-type doping were characterized, including ion implantation and annealing, etching and regrowth, diffusion, and neutron transmutation. Ion implantation induces strain with a depth profile correlated to the implant depth and is recovered after capping and gyrotron microwave annealing, but higher implanted concentrations retain some residual strain. High-pressure annealing can completely recover the strain without the need for capping. For etch and regrowth process, inductively coupled plasma (ICP) etching introduces strain in the GaN material that can be partially recovered by follow-up tertiary butyl chloride (TBCl) etching. Diffusion doping does not introduce new strains in the GaN material while neutron transmutation doping leads to irradiation damage and nucleation of new defects at higher fluence.