The basic interaction mechanism of pulsed laser ablation of tissue reveals a complexity of parameters, such as the optical properties of the tissue and the technical characteristics of the laser beam. The role of the laser wavelength, the pulse duration, the energy fluence, etc. as well as the implications on the beam delivery means, the ablated surface modifications and the diagnostic techniques employed are under investigation. For example, it was experimentally verified that when using mid-infrared lasers with pulse durations in the ns range, the photothermal mechanism involved exhibits strong absorption restricting the residual thermal damage to a relatively small zone. On the other hand the ablation of tissue with ultrashort, picosecond and femtosecond, visible and near-infrared laser pulses has been investigated as an alternative, as the energy threshold for ablation biological tissue, depends approximately on the square root of the pulse duration. However the pulse length shortening creates problems to the fibers or the waveguides ends, due to the very high laser power densities involved. Conventional and advanced microscopy, scanning electron microscopy--SEM and atomic force microscopy--AFM, were used to study the surface and ends alterations of the delivery system involved and the surface alterations of the soft or the hard tissue target in pulsed laser ablation. Finally differentiation between the normal and the pathological tissue was achieved by employing the laser induced fluorescence--LIF diagnostic technique in a long term effort to develop a computer aided system, which will facilitate the automated, real-time characterization of healthy or atherosclerotic plaques in a less invasive laser ablation clinical procedure.