Post-deposition annealing by ultra-short laser pulses can modify the optical properties of SnO2 thin films by means of thermal processing. Industrial grade SnO2 films exhibited improved optical properties after picosecond laser irradiation, at the expense of a slightly increased sheet resistance [Proc. SPIE 8826, 88260I (2013)]. The figure of merit φ = T10 / Rsh was increased up to 59% after laser processing. In this paper we study and discuss the causes of this improvement at the atomic scale, which explain the observed decrease of conductivity as well as the observed changes in the refractive index n and extinction coefficient k. It was concluded that the absorbed laser energy affected the optoelectronic properties preferentially in the top 100-200 nm region of the films by several mechanisms, including the modification of the stoichiometry, a slight desorption of dopant atoms (F), adsorption of hydrogen atoms from the atmosphere and the introduction of laser-induced defects, which affect the strain of the film.