Based on the pure chemical etching, atmospheric plasma processing techniques have been developed for fused silica optics fabrication, in order to achieve deterministic high rate material removal, small tool spot and no mechanical load applied. However, the surface smoothness tends to be deteriorated after etching process. Comprehensive characterization of surface topography after atmospheric plasma processing is necessary in order to understand the opacification phenomenon and etching mechanism. In this paper, a capacitively coupled atmospheric pressure plasma processing (CCAPPP) system and experimental setup are firstly presented. Chemical composition, surface topography, cross-section topography as well as quantitative surface roughness are respectively characterized and analyzed in detail. The results show that the topography difference between the transparent and the opaque area was not caused by chemical composition. The main differences in the microscopic topography were the size and density of etched cellular microstructures. The opacification phenomenon mainly resulted from the excessive roughening on the processed surface topography, causing visible light to be diffusely reflected.