The laser performance and crystalline micro-structural properties of near-infrared step-index channel waveguides fabricated inside Neodymium doped YAG laser ceramics by means of three-dimensional sub-picosecond pulse laser direct writing are reported. Fluorescence micro-mapping of the waveguide cross-sections reveals that an essential crystal lattice re-distribution has been induced after short pulse irradiation. Such lattice re-distribution is evidenced at the waveguide core corresponding to the laser written refractive index increased volume. The waveguides core surroundings also present diverse changes including slight lattice disorder and bi-axial strain fields. The step-index waveguide laser performance is compared with previous laser fabricated waveguides with a stress-optic guiding mechanism in absence of laser induced lattice re-distribution. (C) 2015 AIP Publishing LLC.