The octadecyl–trimethoxysiloxane self-assembled monolayers (SAMs) exhibit better uniformity and smoothness on hydrogenated amorphous carbon (a-C:H) films than on indium tin oxide glasses. The liquid crystal alignment on the SAM/a-C:H can be greatly improved by Ar plasma beam scanning. The pretilt angle increases abruptly with Ar plasma beam scanning time within 5 s and reaches a maximum value of about 5° at a longer scanning time. The surface roughness of SAM slightly increases from 0.10 to 0.13 nm after Ar plasma beam scanning. This implies that bond breaking occurs on the SAM surface during the plasma beam scanning. Fourier transform infrared spectrometer and X-ray photoemission spectroscope data indicate that plasma beam scanning can sputter off the CH2 bonds in the alkyl chain of SAM. The amount of oxygen on the SAM surface increases after plasma beam scanning and the increase of oxygen is attributed to the formation of C–O bonds during air exposure after plasma beam scanning.