Selective control of qubits in a quantum register for the purposes of quantum information processing represents a critical challenge for dense spin ensembles in solid state systems. Here we present a protocol that achieves a complete set of selective single and two-qubit gates on nuclear spins in such an ensemble in diamond facilitated by a nearby NV center. The protocol suppresses internuclear interactions as well as unwanted coupling between the NV center and other spins of the ensemble to achieve quantum gate fidelities well exceeding 99% . Notably, our method can be applied to weakly coupled, distant, spins and therefore represents a scalable procedure that exploits the exceptional properties of nuclear spins in diamond as robust quantum memories.