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We report subnanometer modification enabled by an ultrafine helium ion beam. By adjusting ion dose and the beam profile, structural defects were controllably introduced in a few-layer molybdenum disulfide (MoS2) sample and its stoichiometry was modified by preferential sputtering of sulfur at a few-nanometer scale. Localized tuning of the resistivity of MoS2 was demonstrated and semiconducting, metallic-like, or insulating material was obtained by irradiation with different doses of He(+). Amorphous MoSx with metallic behavior has been demonstrated for the first time. Fabrication of MoS2 nanostructures with 7 nm dimensions and pristine crystal structure was also achieved. The damage at the edges of these nanostructures was typically confined to within 1 nm. Nanoribbons with widths as small as 1 nm were reproducibly fabricated. This nanoscale modification technique is a generalized approach that can be applied to various two-dimensional (2D) materials to produce a new range of 2D metamaterials.