Nanostructured regular patterns on silicon surface are made by using femtosecond laser irradiations. This is a novel method that can modify the surface morphology of any large material in an easy, fast, and low-cost way. We irradiate a solid surface with a 400-nm double frequency beam from an 800-nm femtosecond laser, while the solid surface is submerged in a liquid or exposed in air. From the study of multiple-pulses and single-pulse irradiations on silicon, we find the morphologies of nanospikes and capillary waves to follow the same distribution and periodicity. Thermal transport near the solid surface plays an important role in the formation of patterns; a simulation was done to fully understand the mechanism of the pattern formation in single pulse irradiation. The theoretical models include a femtosecond laser pulse function, a two-temperature model (2-T model), and an estimation of interface thermal coupling. The evolution of lattice temperature over time will be calculated first without liquid cooling and then with liquid cooling, which has not been well considered in previous theoretical papers. The lifetime of the capillary wave is found to be longer than the solidification time of the molten silicon only when water cooling is introduced. This allows the capillary wave to be frozen and leaves interesting concentric rings on the silicon surface. The regular nanospikes generated on the silicon surface result from the overlapping capillary waves.