The authors use a helium ion microscope (HIM) equipped with a tungsten hexacarbonyl gas injection system (GIS) to form tungsten-based pillars on carbon and silicon substrates by helium ion beam-induced deposition. Tungsten-based pillars with a width of ∼40 nm and height of ∼2 μm (aspect ratio of ∼50) are successfully fabricated using the HIM-GIS method. The pillars consist of face-centered cubic WC1-x and/or W2(C, O) grains. Columnar voids with a width of 1–15 nm form in the center of the pillars, suggesting that the pillars are continuously sputter-etched by the incident helium ion beam during deposition. In addition, the authors observe beam irradiation damage in the form of blistering of the Si substrate at the interface between the pillar and Si substrate. The columnar void width and Si blister height decreases as the volumetric growth rate of the pillars increases regardless of the deposition parameters. The authors consider that at least three phenomena compete during pillar formation, namely pillar deposition, sputter-etching, and Si blistering. Although there are numerous parameters involved in HIM-GIS deposition, it appears that the volumetric growth rate determines both the microstructure of the tungsten-based pillars and the degree of substrate damage.