To clarify the ablation mechanism of polytetrafluoroethylene (PTFE) by synchrotron radiation (SR), the effect of the photon energy distribution of an SR beam on the ablation rate was examined. Carbon (C) and a carbon/magnesium fluoride/carbon (C/MgF3/C) membranes were used as filters to modify the photon energy distribution of incident SR beam. The fragments resulting from the decomposition of PTFE by SR irradiation were measured with in situ quadruple mass spectroscopy (QMS). The ablation mechanism of PTFE is due to absorption of the SR by fluorine. In addition, SR ablation was applied to form patterns in metal fluoride films for the first time.