The assembly of individual two-dimensional materials into van der Waals heterostructures enables the construction of layered three-dimensional materials with desirable electronic and optical properties. A core problem in the fabrication of these structures is the formation of clean interfaces between the individual two-dimensional materials which would affect device performance. We present here a technique for the rapid batch fabrication of van der Waals heterostructures, demonstrated by the controlled production of 22 mono-, bi- and trilayer graphene stacks encapsulated in hexagonal boron nitride with close to 100% yield. For the monolayer devices, we found semiclassical mean-free paths up to 0.9 μm, with the narrowest samples showing clear indications of the transport being affected by boundary scattering. The presented method readily lends itself to fabrication of van der Waals heterostructures in both ambient and controlled atmospheres, while the ability to assemble pre-patterned layers paves the way for complex three-dimensional architectures.