Graphene has been used to explore the fascinating electronic properties of ideal two-dimensional carbon, and shows great promise for quantum device architectures. The primary method for isolating graphene, micromechanical cleavage of graphite, is difficult to scale up for applications. Epitaxial growth is an attractive alternative, but achieving large graphene domains with uniform thickness remains a challenge, and substrate bonding may strongly affect the electronic properties of epitaxial graphene layers. Here, we show that epitaxy on Ru(0001) produces arrays of macroscopic single-crystalline graphene domains in a controlled, layer-by-layer fashion. Whereas the first graphene layer indeed interacts strongly with the metal substrate, the second layer is almost completely detached, shows weak electronic coupling to the metal, and hence retains the inherent electronic structure of graphene. Our findings demonstrate a route towards rational graphene synthesis on transition-metal templates for applications in electronics, sensing or catalysis.