The current development of technology makes constant the necessity of getting smaller and smaller features sizes down to micrometer and sub micrometer scales. Laser ablation, which has the great advantage of precise material removal, is a promising candidate. In this dissertation we have demonstrated the feasibility to take advantage of the interaction of femtosecond laser pulses with matter for micro- and nano-structuration and this by having developed a compact and high accurate and flexible apparatus. An analyse of the specific physical mechanisms of laser-matter interaction in the femtosecond regime is presented. Investigations on processing time efficiency as well as the effect of the repetition rate during ablation of metals have been performed. The potential of the multifunctional tool coupled with a compact high repetition rate femtosecond oscillator is shown for different applications in biotechnology. Results on large area mapping as well as accurate nanoprocessing of biological tissue and various materials are presented. This versatile tool covers wide research fields from the nanoprocessing of biological samples as well as the nanostructuring of different type of materials. It is of great interest for many applications in material science, nanobiotechnology and nanomedicine
