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Two commodity polymers, polystyrene (PS) and high-density polyethylene (HDPE), were irradiated by high-energy He ion beams at low fluence to examine the wettability changes at different fluences. The water contact angles of the PS and HDPE surfaces were reduced from 78.3° to 46.7° and 81.5° to 58.5°, respectively, upon increasing the fluence from 0 to 1 × 1013 He2+/cm2 for irradiation durations ≤4 min. Surface analyses were performed to investigate these wettability changes. Surface texture evaluations via scanning electron and atomic force microscopies indicated non-remarkable changes by irradiation. However, the chemical structures of the irradiated polymer surfaces were notable. The high-energy He ions induced nuclear transmutation of C to N, leading to C–N bond formation in the polymer chains. Further, C–O and C=O bonds were formed during irradiation in air because of polymer oxidation. Finally, amide and ester groups were generated by irradiation. These polar groups improved hydrophilicity by increasing surface energies. Experiments with other polymers can further elucidate the correlation between polymer structure and surface wettability changes due to high-energy low-fluence He ion irradiation. This method can realize simple and effective utilization of commercial cyclotrons to tailor polymer surfaces without compromising surface texture and mechanical integrity. [ABSTRACT FROM AUTHOR]