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Two-dimensional (2D) layered materials offer unique properties that make them attractive for continued scaling in electronic and optoelectronic device applications. Successful integration of 2D materials into semiconductor manufacturing requires high-volume and high-precision processes for deposition and etching. Several promising large-scale deposition approaches have been reported for a range of 2D materials, but fewer studies have reported removal processes. Thermal atomic layer etching (ALE) is a scalable processing technique that offers precise control over isotropic material removal. In this work, we report a thermal ALE process for molybdenum disulfide (MoS2). We show that MoF6can be used as a fluorination source, which, when combined with alternating exposures of H2O, etches both amorphous and crystalline MoS2films deposited by atomic layer deposition. To characterize the ALE process and understand the etching reaction mechanism, in situ quartz crystal microbalance (QCM), Fourier transform infrared (FTIR), and quadrupole mass spectrometry (QMS) experiments were performed. From temperature-dependent in situ QCM experiments, the mass change per cycle was −5.7 ng/cm2at 150 °C and reached −270.6 ng/cm2at 300 °C, nearly 50× greater. The temperature dependence followed Arrhenius behavior with an activation energy of 13 ± 1 kcal/mol. At 200 °C, QCM revealed a mass gain following exposure to MoF6and a net mass loss after exposure to H2O. FTIR revealed the consumption of Mo–O species and formation of Mo–F and MoFx═O species following exposures of MoF6and the reverse behavior following H2O exposures. QMS measurements, combined with thermodynamic calculations, supported the removal of Mo and S through the formation of volatile MoF2O2and H2S byproducts. The proposed etching mechanism involves a two-stage oxidation of Mo through the ALE half-reactions. Etch rates of 0.5 Å/cycle for amorphous films and 0.2 Å/cycle for annealed films were measured by ex situ ellipsometry, X-ray reflectivity, and transmission electron microscopy. Precisely etching amorphous films and subsequently annealing them yielded crystalline, few-layer MoS2thin films. This thermal MoS2ALE process provides a new mechanism for fluorination-based ALE and offers a low-temperature approach for integrating amorphous and crystalline 2D MoS2films into high-volume device manufacturing with tight thermal budgets.