Femtosecond laser induced surface modification allows us to functionalize surfaces at a micro and nanometer scale. In particular, ultra-short IR irradiation of Si wafers with laser fluences near ablation threshold can induce different surface structures depending on the number of applied pulses. The results of a detailed comparison of our numerical results with the experimental data sheds light on the mechanisms of the structure formation. Here we examine the formation of the following three types of structures (i) after one or several pulses, resonant, quasi-parallel and periodic structures appear. They are spaced by a distance close to the laser wavelength. Our simulation shows that these structures can be attributed to laser excitation of surface plasmons. (ii) after more irradiations (from X1 to around X2), non-resonant grooves or beads are formed. To model these structures, we consider melting and thermo-capillary instability excitation. (iii) upon a large number (from Y1 to around Y2) of irradiations, cones appear similar to the "black silicon" due to the amplification of the bead structures. The performed analysis is helpful in the explanation of a large number of experiments. The results have a practical application for the development of solar cells, for the change of surface mouillability, etc.