Specimen contamination induced by electron beam irradiation has long been a serious problem for high-resolution imaging and analysis by a transmission electron microscope (TEM). It creates a deposition of carbonaceous compounds on a region under study, causing the loss of resolution. We developed a method to reduce the beam-induced specimen contamination by cleaning a TEM with activated oxygen radicals. The hydrocarbon contaminants accumulated inside the microscope's chamber can be etched away by gentle chemical oxidation without causing any damage to the microscope. The "contamination-free TEM" can effectively suppress the deposition of carbon-rich products on a specimen and therefore enables us to perform high-resolution carbon elemental mapping by energy-filtering transmission electron microscopy (EFTEM). In this study, we investigated the structure of polymer brushes immobilized on a silica nanoparticle (SiNP), of which molecular weight, length, and density of the brushes had been characterized in detail. The isolated particle showed the stretched formations of the polymer chains growing from the surface, while the densely distributed particles showed the connection of the polymer chains between neighboring particles. Moreover, the polymer brush layer and the surface initiator could be differentiated from each other by the component-specific contrast achieved by electron spectroscopic imaging (ESI). The contamination-free TEM can allow us to perform high-resolution carbon mapping and is expected to provide deep insights of soft materials' nanostructures.