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The advancements in producing interactions of concentrated energy fluxes, such as femtosecond lasers and high-energy electron beams with the absorbing substances, have facilitated new discoveries and excitement in various scientific and technological areas. Since their invention, significant improvements in temporal, spatial, energetic, and spectroscopic characteristics have been realized. Due to the ultrashort pulse width and higher intensity (1012 W/cm2), it is possible to ablate the materials with negligible damage outside the focal volume, thereby allowing the treatment of biological samples, such as live cells, membranes, and removal of thin films, as well as bulk materials for many applications in diverse fields, including micro-optics, electronics, and even biology under extremely high precision. Since most biological systems are transparent toward the NIR spectral range, it follows the nonlinear multi-photon absorption interaction mechanism. In contrast, the electron beam follows linear absorption mechanism for material modifications even at lower energies. For realizing the fs-laser nano-processing in material applications, such as silicon microchips, or in biology like retinal cells, it is crucial to find a way to deliver these pulses precisely at the site of action and enhance the selectivity. The utilization of electron beams in material modification has also been exercised widely to attain nanoscale precision. In the next section, biological materials, such as cornea, retina, and silk, are discussed.