Thermal effects produced in a laser-irradiated sample were studied by micro-X-ray diffraction and micro-Fourier transform infrared spectroscopy (FTIR). Gypsum, transformed into bassanite at 124 degrees C and into anhydrite at 147 degrees C, was used as a thermal indicator. Pit formation by a wavelength-tunable free electron laser (FEL) irradiation on the gypsum pellet maximized at a wavelength of 3.0 microm, 2 mJ/shot, and pits were not detected in those irradiated at 2.6 or 3.8 microm compared with the maximum at 3.0 microm and diminished at 2.0 or 4.0 microm in the human tooth case. Micro-X-ray diffraction and micro-FTIR did not reveal any appreciable bassanite or anhydrite in the irradiated regions. From the laser ablation viewpoint, these results allow the FEL ablation to be considered as plasma or evaporative ones. This study indicated that the micro-pulse of laser was effective to prevent thermal damages of laser irradiation.