Surface modification effects on patterned surface with gas cluster ion beam (GCIB) were studied by observation with a cross-sectional transmission electron microscope in order to use it for planarization of patterned media such as discrete track media (DTM) or bit-patterned media (BPM) for future hard disk drives. As a model structure of patterned media, line-and-space or bit patterns were fabricated on Si substrates, and subsequently amorphous carbon films were deposited on them. After Ar-GCIB irradiations on amorphous carbon, it was shown that GCIB preferentially removed bumps or crest on the surface of amorphous carbon at normal incidence. The required thickness for planarization was close to the initial peak-to-valley. At an incident angle of 57°, line-and-space patterns became sharp-pointed shape. On the contrary, line-and-space patterns were planarized without tiny asperity formation at 77°. These results indicate that quite effective planarization of patterned surface is possible using GCIB at normal or glancing angle irradiation.