Wet-chemical-assisted femtosecond (fs) laser ablation has been developed for high-efficiency, high-quality nanofabrication of gallium nitride (GaN) surface. In this technique, an fs laser beam is focused on the surface of a single-crystal GaN substrate immersed in 35% hydrochloric (HCl) acid by a high-numerical-aperture objective lens. This method produced higher quality ablation craters with sharper edges, smoother surfaces, and less residual debris than conventional fs-laser ablation in air followed by etching in HCl (two-step processing method). This is presumably due to a photochemically or photothermally assisted chemical reaction associated with the HCl acid solution. Using the second harmonic of an fs laser (λ = 387 nm), nanocraters with diameters as small as 320 nm (full width at half maximum) were formed at a GaN substrate surface. Assuming that this process is based on two-photon absorption, we theoretically calculated the diameters of ablation craters. The calculation results agree well with the experimental results, particularly in the low-energy region. Multiscan irradiation was performed to fabricate a two-dimensional (2D) array of nanoholes with a high aspect ratio of ~1.6, which is much higher than that obtained using single-pulse irradiation. The aspect ratio was found to depend on the refractive index of the medium above the GaN substrate. The fabricated 2D array of nanoholes on a GaN surface could be used as a 2D photonic crystal for enhancing the light extraction efficiency of GaN-based blue LEDs.© (2010) COPYRIGHT SPIE--The International Society for Optical Engineering. Downloading of the abstract is permitted for personal use only.