Bottom-up block copolymer (BCP) lithography mediated by self-assembly of polystyrene (PS)/poly-methyl methacrylate (PMMA) is widely used as an alternative patterning method for various deep nanoscale devices, such as optical devices and transistors, replacing conventional top-down photolithography. However, the nanoscale BCP mask features formed on the substrates after direct self-assembly of BCP tend to be easily damaged during exposure to the following plasma processing. In this study, silicon masked with a nanoscale BCP mask (PS) was etched by irradiating with a Cl2/Ar neutral beam in addition to a Cl2/Ar ion beam, and the effect of a Cl2/Ar neutral beam instead of a Cl2/Ar ion beam on damage to the PS mask and the silicon etch characteristics of nanodevices was investigated. The results show that the use of a neutral beam instead of an ion beam decreased degradation of the BCP mask during etching; therefore, a more anisotropic silicon etch profile in addition to improved etch selectivity of silicon compared to the BCP mask was observed. Moreover, by using the neutral beam, the sidewall roughness and sidewall angle also improved due to the decreased surface charge and reduced damage to the nanoscale PS mask resulting from use of a highly directional radical beam instead of a conventional ion-based beam.