Surface roughness plays a critical role in ultrashort pulse laser ablation, particularly for industrial applications using burst mode operations, multi-pulse laser processing, and the generation of laser-induced periodic surface structures. Hence, we address the impact of surface roughness on the resulting laser ablation topography, comparing predictions from a simulation model to experimental results. We present a comprehensive multi-scale simulation framework that first employs finite-difference-time-domain simulations for calculating the surface fluence distribution on a rough surface measured by atomic-force-microscopy followed by the two-temperature model coupled with hydrodynamic/solid mechanics simulation for the initial material heating. Lastly, a computational fluid dynamics model for material relaxation and fluid flow is developed and employed. Final state results of aluminum and AISI 304 stainless steel simulations demonstrated alignment with established ablation models and crater dimension prediction. Notably, Al exhibited significant optical scattering effects due to initial surface roughness of 15 nm—being 70 times below the laser wavelength -leading to localized, selective ablation processes and substantially altered crater topography compared to idealized conditions. Contrary, AISI 304 with $${R}_{\text{q}}$$
R
q
surface roughness of 2 nm showed no difference. Hence, we highlight the necessity of incorporating realistic, material-specific surface roughness values into large-scale ablation simulations. Furthermore, the induced local fluence variations demonstrated the inadequacy of neglecting lateral heat transport effects in this context.