Atomic hydrogen generated by the filament in Hot Wire Chemical Vapor Deposition System plays an important role in depositing of thin films. It is believed that the etching process by atomic hydrogen taking place during the deposition process is one of key mechanism to obtain high quality thin films. In order to see a clear effect of interaction of atomic hydrogen with the growth surface, we focused only on the etching process in this system. We used amorphous and crystalline silicon as the substrate and then monitored its etching rate. The etching rate increases with increases of filament temperature due to increasing amount of atomic hydrogen generated on the filament. When substrate temperature increases, the etching rate decreases. We believe this is due to the decrease of the surface coverage of hydrogen with the increase of substrate temperature. The etching rate increases initially with pressure increase and then remains constant with further pressure increase. This phenomenon indicates that there is the competition between the increase in the amount of the atomic hydrogen generated and decrease in the diffusion coefficient of atomic hydrogen to the etching surface when pressure increases. The etching rate increases in the order of amorphous Si > poly-Si > crystalline silicon. This effect plays a key role in the selective deposition in this system.@footnote 1@ In addition, we found that there is preferential crystalline orientation etching (111) < (110) < (100) which can be used to explain the crystalline orientation during deposition of poly-Si films in this system.@footnote 2@ This preferential etching among amorphous phase and crystalline phase with the different orientation can be explained by the amount of dangling bonds in the silicon films. @FootnoteText@ @footnote 1@ S. Yu, E. Gulari and J. Kanicki, Appl.Phys. Lett., 68, 2681 (1996) @footnote 2@ S. Yu, S. Deshpande, E. Gulari and J. Kanicki, Mat. Res. Soc. Symp. Proc., 377, 69 (1995).