In a nanoscale molecular junction at finite bias voltage, the intramolecular distribution of vibrational energy can strongly deviate from the thermal equilibrium distribution and specific vibrational modes can be selectively excited in a controllable way, regardless of the corresponding mode frequency. This is demonstrated for generic models of asymmetric molecular junctions with localized electronic states, employing a master equation as well as a nonequilibrium Green's function approach. It is shown that the applied bias voltage controls the excitation of specific vibrational modes by tuning the efficiency of vibrational cooling processes due to energy exchange with the leads.