Heterostructures formed by stacking layered materials require atomically clean interfaces. However, contaminants are usually trapped between the layers, aggregating into randomly located blisters, incompatible with scalable fabrication processes. Here we report a process to remove blisters from fully formed heterostructures. Our method is over an order of magnitude faster than those previously reported and allows multiple interfaces to be cleaned simultaneously. We fabricate blister-free regions of graphene encapsulated in hexagonal boron nitride with an area ~ 5000 μm2, achieving mobilities up to 180,000 cm2 V-1 s-1 at room temperature, and 1.8 × 106 cm2 V-1 s-1 at 9 K. We also assemble heterostructures using graphene intentionally exposed to polymers and solvents. After cleaning, these samples reach similar mobilities. This demonstrates that exposure of graphene to process-related contaminants is compatible with the realization of high mobility samples, paving the way to the development of wafer-scale processes for the integration of layered materials in (opto)electronic devices.