A hydrogen hyperthermal neutral beam (HNB) generated by an inclined slot-excited antenna electron cyclotron resonance plasma source has been used to etch hydrogenated amorphous silicon (a-Si:H) and polycrystalline silicon (poly-Si) films. In this work, we present selective etching of a-Si:H with respect to poly-Si by hydrogen plasma and hydrogen HNB under various substrate temperatures, gas pressures, and bias voltages of the neutralizer. We have observed that the etch rate of a-Si:H is considerably higher than that of poly-Si. The etch rate is largely dependent upon the substrate temperature. In this experiment, the optimal substrate temperature for improving the etch rate is approximately at 150°C. The root mean square surface roughness of the etched material reaches a maximum at 150°C and decreases rapidly. The etch rate of poly-Si is not sensitive to changes in the experimental condition, such as the substrate temperatures and gas pressures. However, as the hydrogen HNB energy is increased, the etch rate of poly-Si also increases gradually. The hydrogen HNB energy contributes in improving the etch rate of a-Si:H and poly-Si films.