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Nanostructured molybdenum disulfide (MoS2) thin films were grown on a nanohole-patterned silicon substrate using plasma-enhanced atomic layer deposition. A nanoscale hole-patterned silicon substrate was fabricated for the growth of MoS2 film using the self-assembly-based nanofabrication method. The nanoscale holes can significantly increase the surface area of the substrate while the formation and growth of nanostructures normally start at the surface of the substrate. Hydrogen sulfide (H2S) gas was used as the S source in the growth of molybdenum disulfide (MoS2) while molybdenum (V) chloride (MoCl5) powder was used as the Mo source. The MoS2 film had a stoichiometric ratio of 1 (Mo) to 2 (S), and had peaks of E12g and A1g, which represent the in-plane and out-plane vibration modes of the Mo–S bond, respectively. It was found that the MoS2 film grown in the nanoscale hole, especially at the wall of the hole, has more hexagonal-like structures due to the effects of nanoscale space confinement and the nanoscale interface although the film shows an amorphous structure. Post-growth high-temperature annealing ranging from 800 to 900 °C produced local crystalline structures in the film, which are compatible with those reported by other researchers.