By stacking various two-dimensional (2D) atomic crystals1 on top of each other, it is possible to create multilayer heterostructures and devices with designed electronic properties2, 3, 4, 5. However, various adsorbates become trapped between layers during their assembly, and this not only affects the resulting quality but also prevents the formation of a true artificial layered crystal upheld by van der Waals interaction, creating instead a laminate glued together by contamination. Transmission electron microscopy (TEM) has shown that graphene and boron nitride monolayers, the two best characterized 2D crystals, are densely covered with hydrocarbons (even after thermal annealing in high vacuum) and exhibit only small clean patches suitable for atomic resolution imaging6, 7, 8, 9, 10. This observation seems detrimental for any realistic prospect of creating van der Waals materials and heterostructures with atomically sharp interfaces. Here we employ cross sectional TEM to take a side view of several graphene–boron nitride heterostructures. We find that the trapped hydrocarbons segregate into isolated pockets, leaving the interfaces atomically clean. Moreover, we observe a clear correlation between interface roughness and the electronic quality of encapsulated graphene. This work proves the concept of heterostructures assembled with atomic layer precision and provides their first TEM images.