The growth selectivity and structural quality of GaN nanowires obtained by plasma-assisted molecular beam epitaxy on pre-patterned GaN(0001) templates are investigated by means of non-destructive techniques. Optimum control over the nanowire arrangement and size requires a pitch between the mask apertures below twice the diffusion length of Ga atoms. Lower pitches, however, seem to slightly diminish the structural quality of the material, as revealed by the increase of the Raman peak linewidths. The photoluminescence spectra of the nanowires show a considerable presence of basal plane stacking faults, whose density increases for decreasing nanowire diameter. The capabilities of Kelvin probe force microscopy for imaging these kind of defects are also demonstrated.