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.