The influence of laser parameters on silica based waveguide inscription is investigated by using femtosecond laser pulses at 1030 nm (near-IR) and at 343 nm (UV). Negative phase contrast microscopy technique is used to measure the refractive index contrast for different photo-inscribed waveguides and shows the effects of both laser wavelength and scanning speed. In particular, UV photons have a higher efficiency in the waveguide production process as also confirmed by the lower optical losses at 1550 nm in these waveguides. These measurements are combined with micro-Raman and photoluminescence techniques, highlighting that laser exposure induces both structural modification of the silica and point defects generation. The contribution of induced defects to the total refractive index change is singled out by applying two different thermal treatments on the waveguide. The first, up to 500°C, is able to remove the most of the induced non-bridging-oxygen-hole-centers (NBOHCs) while the second up to 750°C erases almost all absorbing induced defects, highlighting the strong contribution of additional defects, not yet identified.