In this paper 3D photofabrication by femtosecond laser pulses and its application in photonics and biomedicine is presented. Recent advances in three-dimensional micro structuring of photosensitive materials by multiphoton illumination technique are presented. Near-infrared Ti:sapphire femtosecond laser pulses (at 800/780 nm) are applied for 3D material processing. When tightly focused into the volume of a UV-photosensitive material they interact with material through two-photon absorption. As a result a highly localised material modification appears. It is a very attractive technology for the fabrication of drug delivery systems and medical implants. In particular, fabrication of microneedle arrays, that allow transdermal drug delivery, has great potential. The application of 2PP for the fabrication of 3D scaffolds directly targets such common issues as vascularization of large in vitro grown tissues, and demand for patient specific scaffold production.