Organic materials have been widely used in various fields of electronic applications. However, they are difficult to process without damage by using a conventional ion beam which use energetic ions. In this study, gas cluster ion beam (GCIB), which shows low-damage process, was used for organic materials, and irradiation effect of size selected GCIB was studied with Xray photoelectron spectroscopy (XPS). In the case of irradiation of 500 eV Ar ion (monomer ion) on polyimide, the intensities of both N-C=O and C-O bond decreased after irradiation. On the other hand, there was small change in the XPS spectra after 15 keV Ar-GCIB irradiation with the same ion dose. The etching rate of polyimide per one ion with 15 keV Ar-GCIB was almost 1.8×104 times higher than that with 500 eV Ar monomer ions. The damages in polyimide decreased with increasing the Ar cluster size owing to the reduction of energy per atom at acceleration voltage of 15 kV. After irradiation of size selected 5 kV Ar cluster ion, damage was almost negligible. Although, the surface became rough after irradiation of Ar-GCIB, surface roughness and the change of chemical bond were very small with N2-GCIB irradiation. Ar-GCIB irradiation on dye-sensitized solar cells (N719) showed that very low-damage process is possible with GCIB, and it indicated that GCIB is suitable for surface processing of organic materials used in electronic devices.