Intercalation of C60 molecules at the graphene-substrate interface by annealing leads to amorphous and crystalline intercalated structures. A comparison of topography and electronic structure with wrinkles and moiré patterns confirms intercalation. The intercalated molecules imprint a local strain/deformation on the graphene layer, whose magnitude is controlled by the intermolecular distance. The crystalline intercalated structure exhibits a superlattice peak in the local density of states. This work provides control of local strain in graphene.