Atomically thin semiconductors have dimensions that are commensurate with critical feature sizes of future optoelectronic devices defined using electron/ion beam lithography. Robustness of their emergent optical and valleytronic properties is essential for typical exposure doses used during fabrication. Here, we explore how focused helium ion bombardment affects the intrinsic vibrational, luminescence and valleytronic properties of atomically thin MoS$_{2}$. By probing the disorder dependent vibrational response we deduce the interdefect distance by applying a phonon confinement model. We show that the increasing interdefect distance correlates with disorder-related luminescence arising 180 meV below the neutral exciton emission. We perform ab-initio density functional theory of a variety of defect related morphologies, which yield first indications on the origin of the observed additional luminescence. Remarkably, no significant reduction of free exciton valley polarization is observed until the interdefect distance approaches a few nanometers, namely the size of the free exciton Bohr radius. Our findings pave the way for direct writing of sub-10 nm nanoscale valleytronic devices and circuits using focused helium ions.
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