A status report on rapidly advancing femtosecond laser technology, three-dimensional (3D) microstructuring by multiphoton illumination technique, is given. Taking its origin from multiphoton microscopy, this technique is now becoming an important microfabrication tool. In our work we apply near-infrared Ti:sapphire femtosecond laser pulses (at 800/780 nm) for 3D material processing. When tightly focused into the volume of a photosensitive material (or photoresist), they initiate 2PP process by, for example, transferring liquid into the solid state. This allows the fabrication of any computer generated 3D structure by direct laser “recording” into the volume of photosensitive material. 2PP of photosensitive materials irradiated by femtosecond laser pulses is now considered as enabling technology for the fabrication of 3D photonic crystals and photonic crystal templates. In particular, 2PP allows one to introduce defects at any desired locations, which is crucial for the practical applications. Recently, we studied possible applications of 2PP technique in biomedicine. 2PP is a very interesting technique for the fabrication of drug delivery systems, scaffolds for tissue engineering, and medical implants. These and other biomedical applications of 2PP will be reviewed.