Surface morphology and structural changes upon femtosecond laser ablation from crystalline silicon (001)were examined ex-situ by optical, scanning electron, and atomic force microscopy, as well as Raman spectroscopy. After repetitive illumination with several thousand laser pulses at an intensities below or near the single shot damage threshold (2x10(12) W/cm(2)), self-assembled periodic nanostructures; with periods of 200 nm resp. 600-700 nm develop at the crater bottom. Micro-Raman spectroscopy reveals phase transformations inside the crater from Si-I to the polymorphs Si-III, Si-XII, hexagonal Si-wurtzite (Si-IV), and amorphous silicon, pointing to substantial pressure and volume changes during the interaction. The ablation dynamics was monitored by time-of-flight mass spectroscopy, showing the emission of superthermal positive ions with a kinetic energy of several eV as well as significant contributions at lower kinetic energies. The results suggest that the ablation is associated with considerable recoil pressure and leaves behind a severely perturbed crystal surface. The resulting instability relaxes by a self-organization, independent of the initial, and surrounding, crystal structure.