A mass filter for an ion beam system includes at least two stages and reduces chromatic aberration. One embodiment includes two symmetrical mass filter stages, the combination of which reduces or eliminates chromatic aberration, and entrance and exit fringing field errors. Embodiments can also prevent neutral particles from reaching the sample surface and avoid crossovers in the beam path. In one embodiment, the filter can pass a single species of ion from a source that produces multiple species. In other embodiments, the filter can pass a single ion species with a range of energies and focus the multi-energetic ions at the same point on the substrate surface.