We propose and analyze a nanomechanical architecture where light is used to perform linear quantum operations on a set of many vibrational modes. Suitable amplitude modulation of a single laser beam is shown to generate squeezing, entanglement and state transfer between modes that are selected according to their mechanical oscillation frequency. Current optomechanical devices based on photonic crystals, as well as other systems with sufficient control over multiple mechanical modes, may provide a platform for realizing this scheme.