The synthesis of metal nanoparticles (NPs) using microfluidic reactors has become a major method for limiting reagent consumption and achieve a precise control of the morphological properties. Failure in realizing the reproducibility of the results is mostly associated with the accumulation of metallic nanostructures on the walls of the microfluidic devices, periodically removed by acid treatment. In this study, we show that ns-pulsed laser ablation (PLA) in water can be a safe, effective, and green method for the regeneration of clogged microfluidic reactors. The effect of the laser-pulse fluence on the removal of metallic nanostructures was studied for the first time on silver (Ag) thin films with a thickness of 50 nm deposited over SiO2 substrates, using 3-mercaptopropyl trimethoxysilane as a chemical adhesion layer. As point of novelty, the experimental results show that at low fluence (F < 0.1 J/cm2), ablation is principally caused by delamination of the thin film associated with the thermoelastic force while thermal processes inducing phase conversion of the metal dominate at higher fluence. Low-fluence regimes are better suited for the single-pulse removal of the nanomaterial, whereas in high F regimes, we observed melting and recondensation of the metal on the SiO2 surface so that multiple pulse interactions were necessary for complete ablation of the thin film. For the delamination and the phase transformation processes, the threshold fluences were 3.7 × 10−2 and 7.0 × 10−2 J/cm2, respectively. The experimental setup in the thermoelastic PLA regime was applied to unclog glass microfluidic devices used for synthesizing citrate-stabilized AgNPs. Using this simple and easily achievable laser-scanning experimental configuration, we demonstrated that PLA in water is a reliable and efficient technique, with results comparable to acidic treatment in terms of efficiency and time necessary for the complete removal of the Ag nanomaterial.