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Electrical beam (EB) irradiation is used to chemically modify the amorphous carbon film, a-C:H, which is prepared by the DC magnetron sputtering. The starting a-C:H film has vague columnar structure with lower density intercolumns as predicted by Thornton structure model. The EB-irradiated a-C:H film has fine nano-columnar structure with the average columnar size of 10–15 nm. This size is equivalent to the measured in-plain correlation length by the Raman spectroscopy. Little change in the sp2/sp3 bonding ratio is observed in the columnar matrix before and after EB-irradiation. Increase of sp2/sp3 ratio is noted in the intercolumns of irradiated a-C:H films. No change is detected in the hydrogen content of a-C:H films before and after EB-irradiation: 35 at% hydrogen in a-C:H. Increase of the in-plain density via EB-irradiation, is attributed to the increase of local atomic density in the intercolumns, which is measured by the electron energy zero-loss spectroscopy. This local densification is accompanied with ordering or graphitization in the intercolumns of the EB-irradiated a-C:H film. The nano-columnar a-C:H film modified by EB-irradiation has non-linear elasticity where indentation displacement should be reversible up to 8% of film thickness. Owing to this ordering and densification via EB-irradiation, softening both in stiffness and hardness takes place with increasing the irradiation time.