In this study, atmospheric-pressure (AP) plasma generated using He/O2/CF4 mixture as feed gas was used to etch the single-crystal silicon (100) wafer and the characteristics of the etched surface were investigated. The wafer morphology and surface elemental composition were analyzed using scanning electron microscope (SEM) and X-ray photoelectron spectroscopy (XPS), respectively. The XPS results reveal that the fluorine element will be deposited on the wafer surface during the etching process when oxygen was not introduced as the feed gas. By detecting the energy and intensity of emitted particles, optical emission spectroscopy (OES) is used to identify the radicals in plasma. The fluorocarbon radicals generated during CF4 plasma ionization can form carbon fluoride polymer, which is considered as one factor to suppress the etching process. The roughness was measured to be changed with the increase in the etching time. The surface appears to be rougher at first when the plasma etching occurred on the subsurface damaged (SSD) layer, and the subsurface cracks would show on the surface after a short-time etching. After the damaged layer was fully removed, etching resulted in the formation of square-opening etching pits. During extended etching, the individual etching pits grew up and coalesced with one another; this coalescence provided an improved surface roughness. This study explains the AP plasma etching mechanism, and the formation of anisotropic surface etching pits at a microscale level for promoting the micromachining process.