We report on the structural investigation of self- organized periodic microstructures (ripples) generated in Si (100) targets after multishot irradiation by approximately 100-fs to 800-nm laser pulses at intensities near the single shot ablation threshold. Inspection by surface sensitive microscopy, e.g., atomic force microscopy (AFM) or scanning electron microscopy (SEM), and conventional and high-resolution transmission electron microscopy re- veal complex structural modifications upon interaction with the laser: even well outside the ablated area, the target surface exhibits fine ripple-like undulations, consisting of alternating crystalline and amorphous silicon. Inside the heavily modified area, amorphous silicon is found only in the valleys but not on the crests which, instead, consist of highly distorted crystalline phases, rich in defects.