AuPd nanoparticles are formed on fluorine-doped tin oxide (FTO) by a nanosecond laser irradiation-induced dewetting process of deposited AuPd films. In particular, we analyze the effect of the surface topography of the substrate on the dewetting process and, so, on the final mean size of the formed nanoparticles. In fact, we used two supporting FTO substrates differing in the surface topography: we used a FTO layer which is un-intentionally patterned since it is formed by FTO pyramids randomly distributed on the glass slide as result of the deposition process of the same FTO layer, namely substrate A. We used, also, a further FTO substrate, namely substrate B, presenting, as a result of a chemical etching process, a higher roughness and higher mean distance between nearest-neighbor pyramids with respect to substrate A. The results concerning the size of the obtained AuPd NPs by the laser irradiations with the laser fluence fixed shows that the substrate topography impacts on the dewetting process. In particular, we found that below a critical thickness of the deposited AuPd film, the NPs formed on substrates A and B have similar size and a similar trend for the evolution of their size versus the film thickness (i.e., the dewetting process is not influenced by the substrate topography since the film does not interact with the substrate topography). On the other hand, however, above a critical thickness of the deposited AuPd film, the AuPd NPs show a higher mean size (versus the film thickness) on substrate B than on substrate A, indicating that the AuPd film interacts with the substrate topography during the dewetting process. These results are quantified and discussed by the description of the substrate topography effect on the excess of chemical potential driving the dewetting process.