In this study the sections of human tissues were treated under 9.5 μm FEL in the BFEL based on the vibrational spectroscopic investigation that significant differences occur between normal and malignant tissues. Under the defocus condition, the burning of tissue section at some part while other part remains unchanged, suggesting that the FEL can selectively destroy some part of tissue. Vibrational spectroscopic and microscopic methods have shown that the FEL can induce decomposition of malignant tissues. The application of FEL whose wavelength is on the characteristic bands of malignant tissues may provide a new method to kill cancer cells with higher selectivity. For understanding the interactions between FEL and biological tissues, structure changes of substances under irradiation by FEL of 9.414 μm and 6.228 μm were measured using FTIR spectroscopy. The samples include ATP, ADP, AMP, and D-ribose, etc. The FTIR spectra of the molecules before and after irradiation of FEL indicate molecular structure variations of the samples after irradiation of FEL, especially the rearrangement of their hydrogen bond networks, which may be caused by multiple photons process induced by FEL.