Amorphous regions in sapphire with sub-micrometer 3D resolution have been produced at the focus of a single femtosecond laser pulse. Crystalline-to-amorphous and amorphous-to-polycrystalline transitions (crystalline and amorphous regions are marked C and A in the HRTEM image) are induced by single- and multi-pulse irradiation, respectively. The wet-etching selectivity for the amorphous phase is significantly greater than that for the crystalline phase in aqueous HF.