Functional surfaces characterised by periodic microstructures are sought in numerous technological applications. Direct laser interference patterning (DLIP) is a technique that allows the fabrication of microscopic periodic features on different materials, e.g., metals. The mechanisms effective during nanosecond pulsed DLIP of metal surfaces are not yet fully understood. In the present investigation, the heat transfer and fluid flow occurring in the metal substrate during the DLIP process are simulated using a smoothed particle hydrodynamics (SPH) methodology. The melt pool convection, driven by surface tension gradients constituting shear stresses according to the Marangoni boundary condition, is solved by an incompressible SPH (ISPH) method. The DLIP simulations reveal a distinct behaviour of the considered substrate materials stainless steel and high-purity aluminium. In particular, the aluminium substrate exhibits a considerably deeper melt pool and remarkable velocity magnitudes of the thermocapillary flow during the patterning process. On the other hand, convection is less pronounced in the processing of stainless steel, whereas the surface temperature is consistently higher. Marangoni convection is therefore a conceivable effective mechanism in the structuring of aluminium at moderate fluences. The different character of the melt pool flow during DLIP of stainless steel and aluminium is confirmed by experimental observations.