Nanoprocessing of materials using ultrashort laser pulses involves a number of concurrent fundamental physical processes. Due to different time and spatial scales of activation, however, these processes are difficult to study within the frames of a single computational model on one hand, and yet not possible to isolate in the experimental analysis on the other hand. In their detailed investigation, the transient character of the nonequilibrium states of matter induced with a short laser pulse hampers the applicability of continuum approaches, but classical molecular dynamics simulations are usually limited in the system sizes. In this work, a molecular dynamics based model coupled to a continuum description of the photo-excited free carrier's dynamics and implemented in parallel algorithm is extended to the scale directly accessible in the experiment. This allows for the first time a direct comparison to experimental data. The essential mechanisms responsible for the sh ort laser pulse surface nanostructuring are analyzed in the complex dynamics of competing processes simultaneously involved into the nanostructures generation process. The modeling and experiment show a very good agreement and predict a new opportunity for fabrication of nanoparticle structures and the surface subpatterning.