Biomedical applications of vibrational spectroscopy developed for routine analysis reqiure reliable methods for data evaluation. Artificial neural networks open a new perspective for the spectra differentiation and identification of biological samples with their small spectra variance. In the present study, the stacked spectral data processing and the following use of neural networks for spectral identification was investigated. 6 different neural network architectures were tested in their capability to built spectral libraries for different bacterial genera and for yeasts, using FT-IR and FT-Raman spectra. After developing these libraries, they were connected to a large library, what we called "multilayered neural networks". This combines the advantages that the wavelength can be choosen more selective for a given differentiation problem and the network architecture and training function can be more adapted to a special task.