The vertical gate-all-around (VGAA) metal-oxide-semiconductor field-effect transistor (MOSFET) holds remarkable potential in the three-dimensional (3D) integrated circuits (ICs), primarily owing to its capacity for vertical integration. The Si nanopillar, a crucial channel in the VGAA MOSFET, is conventionally shaped via the reactive ion etching (RIE) system employing SF6/O2. Past studies have indicated that high O2 gas conditions in RIE often result in “Si grasses,” irregular nanostructures, such as nanospikes on the bottom surface, due to over-passivation. However, this study revealed that ultrahigh O2 proportions (> 70%), especially when combined with low chamber pressure, inhibit the development of Si grasses in the RIE system (termed as super passivation). Nevertheless, this scenario leads to the segmentation of the Si nanopillar. To address this issue, a proposed partial sacrificing method, achieved by sacrificing the upper segment of the nanopillar through prolonged processing time and reduced mask size, successfully yielded Si nanopillars without Si grasses. Furthermore, an empirical model was developed to elucidate how experimental parameters influence etching characteristics, encompassing etching rate and Si nanopillar shape, through a systematic examination of the RIE etching process. This research significantly contributes to the production of VGAA MOSFETs and 3D ICs.