Catalyst-free GaN nanorod regular arrays have been realized by reactive magnetron sputter epitaxy. Two nanolithographic methods, nanosphere lithography (NSL) and focused ion beam lithography (FIBL), were applied to pattern Si substrates with TiNx masks. The growth temperature was optimized for achieving selectivity and well-faceted nanorods grown onto the NSL-patterned substrates. With increasing temperature from 875 to 985 degrees C, we observe different growth behaviors and associate them with selective insensitive, diffusion-dominated, and desorption-dominated zones. To further achieve site-specific and diameter control, these growth parameters were transferred onto FIBL-patterned substrates. Further investigation into the FIBL process through tailoring of milling current and time in combination with varying nanorod growth temperature, suggests that minimization of mask and substrate damage is the key to attain uniform, well-defined, single, and straight nanorods. Destruction of the mask results in selective area growth failure, while damage of the substrate surface promotes inclined nanorods grown into the openings, owning to random oriented nucleation.