Substrate surface preparation is a key step in coating deposition process. In recent years, pulsed laser cleaning has emerged as a possible technique to challenge the traditional preparation methods (based on degreasing and eventually grit-blasting). The laser operated at short-pulse mode offers high cleaning efficiency and therefore has been largely used. In a specific process named PROTAL®, a nanosecond pulsed laser is introduced to prepare the surface simultaneously to thermal spraying, with the purpose of eliminating the contaminants and generating favorite surface conditions for coating deposition. This study aims at clarifying some fundamental aspects of nanosecond pulsed Nd:YAG laser irradiation effects on metallic substrates. Both morphological and chemical surface modifications of titanium alloy as well as aluminum alloys were investigated by optical and scanning electron microscopy, roughness measurements and SIMS. The formation of dispersed craters, which is due to the preferential laser ablation on the superficial defects, dominates the surface modifications. This phenomenon becomes more pronounced when increasing the laser energy density or laser pulse numbers. It presents a significant influence on the roughness of polished surface. For titanium alloy, surface oxidation takes place during the laser irradiation in ambient atmosphere, which smoothes the surface.