Small-scale optical and mechanical components and machines require control over three-dimensional structure at the microscale. Inspired by the analogy between paper and two-dimensional materials, origami-style folding of atomically thin materials offers a promising approach for making microscale structures from the thinnest possible sheets. In this Letter, we show that a monolayer of molybdenum disulfide (MoS2) can be folded into three-dimensional shapes by a technique called capillary origami, in which the surface tension of a droplet drives the folding of a thin sheet. We define shape nets by patterning rigid metal panels connected by MoS2 hinges, allowing us to fold micron-scale polyhedrons. Finally, we demonstrate that these shapes can be folded in parallel without the use of micropipettes or microfluidics by means of a microemulsion of droplets that dissolves into the bulk solution to drive folding. These results demonstrate controllable folding of the thinnest possible materials using capillary origami and indicate a route forward for design and parallel fabrication of more complex three-dimensional micron-scale structures and machines.