The possibility to fabricate microstructures to be used in the medical field is a reality. Further steps in this direction consist in the fabrication of active microstructures for implants and/or for cellular treatments. Two major areas of interest will be briefly treated here. The first is the one of stimulus-responsive optical polymers, especially hydrogels, that can be shaped by means of laser 3D printing and ablation. These can be used for thermal stimulation, energy transduction and sensing. The composition of these polymeric blends is an essential parameter to tune their properties as actuators and/or sensing platforms and to determine the elasto-mechanical characteristics of the printed hydrogel. A second field of interest is the microfabrication of rigid microstructures that can stand the tissue-induced stresses in implants. The increasing demand of microdevices for nanomedicine and personalized medicine has fostered the quest for an efficient combination of composite and hybrid photo-responsive materials and digital micro/nano-manufacturing. Existing works have exploited multiphoton laser photo-polymerization to obtain fine 3D microstructures in hydrogels in an additive manufacturing approach or exploited laser ablation of preformed hydrogels to carve 3D cavities. The aim of this report is to provide a short overview of the basics of photo-polymerization induced by two-photon excitation and to discuss two case studies. In the first one, we discuss the most recent and prominent results in the field of multiphoton laser direct writing of biocompatible hydrogels that embed active nanomaterials not interfering with the writing process and endowing the biocompatible microstructures with physically or chemically activable features such as photo-thermal activity, chemical swelling and chemical sensing. In the second case, we outline the fabrication steps and the first tests of a novel chip which aims at enabling longitudinal studies of the reaction to the biomaterial implant. The chip is composed of a regular reference microstructure fabricated via two-photon polymerization in SZ2080 resist. The geometrical design and the planar raster spacing largely determine the mechanical and spectroscopic features of the microstructures. The development, in vitro characterization and in vivo validation of the Microatlas is performed in living chicken embryos by fluorescence microscopy 3 and 4 days after the implant; the quantification of cell infiltration inside the Microatlas demonstrates its potential as novel scaffold for tissue regeneration. Altogether, the report aims at giving an introduction to the field of nonlinear excitation fabrication and of its impact in the biomedical field.