While the application of focused ion beam (FIB) techniques has become a well-established technique in research and development for patterning and prototyping on the nanometer scale, there is still a large underused potential with respect to the usage of ion species other than gallium. Light ions in the range of m = 1–28 u (hydrogen to silicon) are of increasing interest due to the available high beam resolution in the nanometer range and their special chemical and physical behavior in the substrate. In this work, helium and neon ion beams from a helium ion microscope are compared with ion beams such as lithium, beryllium, boron, and silicon, obtained from a mass-separated FIB using a liquid metal alloy ion source (LMAIS) with respect to the imaging and milling resolution, as well as the current stability. Simulations were carried out to investigate whether the experimentally smallest ion-milled trenches are limited by the size of the collision cascade. While He⁺ offers, experimentally and in simulations, the smallest minimum trench width, light ion species such as Li⁺ or Be⁺ from a LMAIS offer higher milling rates and ion currents while outperforming the milling resolution of Ne⁺ from a gas field ion source. The comparison allows one to select the best possible ion species for the specific demands in terms of resolution, beam current, and volume to be drilled.