Advanced fabrication methods with high efficiency are needed to meet the rising demand for precision optical components. This study proposes a plasma-based isotropic polishing method to remove fused silica's surface defects and subsurface damaged layers. Hence, a medium-pressure plasma process is developed to serve this purpose. The qualitative analysis of the plasma and atom emission spectrum explores the plasma generation and scattering of the activated fluorine (F*) radicals inside the plasma chamber. Material removal rate (MRR) and surface roughness variations with different total pressures of 5–30 mbar and substrate dimensions (i.e., varying length between 5 and 45 mm with fixed width and thickness of 5 and 2 mm) at fixed process parameters, i.e., radio-frequency power of 80 W, pressure ratio of 1:1, gas composition of 90:10, have been investigated. The highest and lowest MRR, i.e., 0.039 mm3/min and 0.0061 mm3/min, are achieved at 5 and 30 mbar total pressures on substrates having lengths 45 and 5 mm, respectively. The highest and lowest percentage change in surface roughness observed are 86.4 % and 17.1 % at 5 mbar and 30 mbar for substrates with 5 and 45 mm lengths, respectively. Surface morphology analysis shows the micro-cracks are reduced after plasma processing. The presence of elements, i.e., F and C, through EDX analysis, confirms the reactions on the plasma processed surface. Moreover, The XPS findings demonstrated that minimal radicals could be incorporated onto the fused silica surface during He/O2/SF6 plasma processing. At lower pressure, the surface roughness value increases due to the increased excitation and ionization rate caused by more interaction between the fluorine and surface atoms. The MRR increases with substrate dimension with constant pressure. Larger substrate dimensions result in increased MRR at lower pressure.