The structural defect of silicon oxide (SiO2) on silicon was evaluated by the infiltration, through the pinhole, of reactive hydrocarbon radicals formed from CH4/H-2 using a tungsten hot filament. Operating conditions like methane concentration, infiltration time, and substrate temperature were studied to map out the pinholes by the diffusion of the reactants and carbonization of the silicon surface. We could measure the number density of pinholes in the SiO2 film by observing carbonized silicon spots on the silicon surface with scanning electron microscopy and atomic force microscopy after removing the oxide film in the buffered HF solution. The number of pinholes could effectively be measured at the temperature below 450 degrees C and methane concentration below 5 volume percent with the appropriate infiltration time. At higher temperature and CH, partial pressure, pinhole was not effectively mapped out due to the deposition of carbon on the top of the oxide surface. The result of the hot filament infiltration measurement was compared with conventional characterization methods such as I-V and etch rate measurements.