In our study we investigate and report the femtosecond pulsed laser deposition of biological and biocompatible materials. Teflon, polyhydroxybutyrate, polyglycolic-acid, pepsin and tooth in the form of pressed pellets were used as target materials. Thin layers were deposited using pulses from a femtosecond KrF excimer laser system (FWHM = 450 fs, lambda = 248 nm, f = 10 Hz) at different fluences: 0.6, 0.9, 1.6, 2.2, 2.8 and 3.5 J/cm(2), respectively. Potassium bromide were used as substrates for diagnostic measurements of the films on a FTIR spectrometer. The pressure in the PLD chamber was 1 x 10(-3) Pa, and in the case of tooth and Teflon the substrates were heated at 250 degrees C. Under the optimized conditions the chemical structure of the deposited materials seemed to be largely preserved as evidenced by the corresponding IR spectra. The polyglycolic-acid films showed new spectral features indicating considerable morphological changes during PLD. Surface structure and thickness of the layers deposited on Si substrates were examined by an atomic force microscopy (AFM) and a surface profilometer. An empirical model has been elaborated for the description of the femtosecond PLD process. According to this the laser photons are absorbed in the surface layer of target resulting in chemical dissociation of molecules. The fast decomposition causes explosion-like gas expansion generating recoil forces which can tear off and accelerate solid particles. These grains containing target molecules without any chemical damages are ejected from the target and deposited onto the substrate forming a thin layer.