A two-step treatment by argon (Ar) and hydrogen plasma beam scanning was developed to modify the surface bonds of a hydrogenated amorphous carbon (a-C:H) film on indium tin oxide glass. The modified a-C:H film is an excellent layer for liquid crystal alignment, on which the pretilt angle of a nematic liquid crystal (ZLI-2293) can be adjusted by the two-step scanning treatment. The chemical bonding characteristics of the as-scanned a-C:H films were measured using micro-Raman and x-ray photoemission spectroscopies. The antiparallel cells were filled with the nematic liquid crystal on the as-scanned a-C:H film to measure the pretilt angle. Experimental results indicate that the carbon dangling bonds are generated through a bond-breaking process during the Ar plasma beam scanning step (first step). The hydrogen plasma beam scanning step (second step) can passivate some of the carbon dangling bonds that are generated in the first step. The pretilt angle decreases as the hydrogen plasma beam scanning time increases. The decrease of pretilt angle is due to the formation of C–H bonds that passivate the a-C:H film and limit the formation of C–O bonds in air.