Periodic ripples of amplitude ∼15 nm were formed in suspended bilayer graphene after nanoindentation with incremental forces up to 600 nN. The structure was annealed at ∼620 K in high vacuum and the corresponding modifications in the mechanical properties and surface morphology were investigated. The pre-tension of the pristine sample was found to be 1.46 N m-1 and after annealing it was reduced to 0.72 N m-1. The nanometre-sized ripples induced by mechanical excitation were found to be flattened after annealing. Tailoring surface corrugations in bilayer graphene through nanoindentation and thermal engineering of these ripples thus provides an innovative fabrication route for flexible electronic devices and strain sensors.