We study the degradation process of closely spaced silver and gold nanocubes under high-energy electron beam irradiation using transmission electron microscopy (TEM). The high aspect ratio gaps between silver and gold nanocubes degraded in many cases as a result of protrusion and filament formation during electron beam irradiation. We demonstrate that the molecular coating of the nanoparticles can act as a protective barrier to minimize electron -beam-induced damage on passivated gold and silver nanoparticles.