Bulk femtosecond laser micromachining  results from laser-induced optical breakdown in the bulk of a transparent material, a process by which optical energy is transferred to the material, ionizing a large number of electrons, which, in turn, transfer energy to the lattice. As a result of the irradiation, the material can undergo a phase or structural modification, leaving behind a localized permanent change in index of refraction or even a void. Femtosecond laser micromachining of transparent materials offers unique advantages over other photonic device fabrication techniques. First, the nonlinear nature of the absorption confines any induced changes to the focal volume. This spatial confinement, combined with laser beam scanning or sample translation, makes it possible to micromachine geometrically complex structures in three dimensions. Second, the absorption process is material independent, allowing for optical devices to be fabricated into compound substrates of different materials. Third, femtosecond micromachining can be used for the fabrication of an optical motherboard, where all interconnects are fabricated before (or even after) bonding multiple photonic devices to a single transparent substrate.
Femtosecond laser irradiation of absorbing surfaces has been an active area of materials science research that has led to a number of unexpected observations and the formation of new materials.  Starting in the late 1970s picosecond studies and later femtosecond pumpprobe studies have been used to elucidate the specific mechanism of many processes, including electron-hole plasma formation, melting,, ablation, and ultrafast melting. Ultrafast melting the disordering of a cold lattice within 100 fs of excitation due to covalent bond weakening upon excitation of more than 15% of the valence electrons is a phenomenon unique to irradiation with high intensity femtosecond laser pulses because these pulses are shorter than the electron-phonon relaxation time. Technologically, ultrashort laser irradiation offers an alternative method for annealing ion-implanted semiconductors.
Early research on the surface morphology resulting from picosecond laser irradiation near the melting threshold revealed the formation of ripples on the surface with a wavelength related to the wavelength of the laser. These so-called Laser Induced Periodic Surface Structures (LIPSS) are similar to ripple structures observed on a variety of materials after irradiation with one or more pulses from a wide range of laser systems (including femtosecond, picosecond and nanosecond pulses) and are well understood. More recently, a number of groups have reported the formation of micro and nano-sized structures resulting from irradiation with femtosecond laser pulses. For the past ten years, we have extensively studied the surface morphology and subsequent properties of silicon surfaces irradiated with femtosecond laser pulses in a variety of environments. About ten years ago, we published the initial discovery that a flat silicon surface is transformed into a forest of quasi-ordered micrometer-sized conical structures upon irradiation with several hundred femtosecond laser pulses in an atmosphere of sulfur hexafluoride (SF6). Shortly afterward, we reported the dependence of cone height on laser fluence and pulse duration. In the subsequent years we studied the ability of the microstructured surfaces to absorb nearly all incident light in the ultraviolet, visible and near-infrared (2502500 nm) as a result of sulfur being trapped in the material during irradiation and successfully employed the process to create silicon-based infrared photodetectors.
The intersection of materials research and ultrafast optical science is producing many valuable fundamental scientific results and applications, and the trend is expected to evolve as new and exciting discoveries are made. Femtosecond laser micromachining presents unique capabilities for three-dimensional, material-independent, sub-wavelength processing. At the same time the surface processing of materials permits the creation of novel materials that cannot (yet) be created under other conditions.
 S. K. Sundaram and Eric Mazur, Nature Materials, 1, 217-224 (2002).
 Rafael R. Gattass and Eric Mazur, Nat. Phot., 2, 219-225 (2008).
 Brian R. Tull, James E. Carey, Eric Mazur, Joel McDonald and Steven M. Yalisove, Mat. Res. Soc. Bull., 31, 626-633 (2006).