The possibility to engineer the van der Waals interactions between graphene layers is crucial for controlling the electronic properties. Using epitaxial graphene with preferential orientations grown on the C-face 6H-SiC as a prototype, we have addressed the annealed structural reconfiguration of graphene layer in view of the evolutions of surface ripples and relative rotation angle (RRA) between lattices. It was found that the heat treatment of graphene layers under vacuum deformed the arcuate ripple surface and subsequently split one ripple into parallel twin pleats, which drastically increased the strains in the films. The originally oriented graphene layers, with small RRA between adjacent layers, were rearranged by the annealing resulting in disordered orientations and larger RRA. After a sufficient annealing, the compressive stress stored in the films was well released to give undistorted graphene lattices. The vacuum annealing is an effective treatment for irreversibly relaxing the graphene structure.