We have studied nano-patterning of a two-dimensional (2D) material with an ultrafine helium ion beam considering shape-, size- and damage-control. The study reveals that the crystalline structure plays an important role in shape-control. Instead of commonly circular-shaped nanopores, spot irradiation onto a single layer of molybdenum disulfide (MoS2) gives rise to a rhombus-shaped nanopore, which is well explained by the sub-rhombus crystalline structure of MoS2. Helium ion beams also show promising capability to precisely control size using a delivered dose. However, the size of the nanopores is not linear with the delivered dose, due to the Gaussian distributed intensity profile of the helium ion beam. The intensity profiles are further estimated by considering aperture size, those results could be taken as a significant reference for size-control. In addition, we clarify that most of the damage is a result of re-deposition, thus controlling re-deposition might be a useful way to alleviate the damage.