Encapsulation of metal nanoparticles just below the surface of a prototypical layered material, graphite, is a recently discovered phenomenon. These encapsulation architectures have potential for tuning the properties of two-dimensional or layered materials, and additional applications might exploit the properties of the encapsulated metal nanoclusters themselves. The encapsulation process produces novel surface nanostructures and can be achieved for a variety of metals. Given that these studies of near-surface intercalation are in their infancy, these systems provide a rich area for future studies. This Review presents the current progress on the encapsulation, including experimental strategies and characterization, as well as theoretical understanding which leads to the development of predictive capability. The Review closes with future opportunities where further understanding of the encapsulation is desired to exploit its applications.