We propose an efficient method to filter out single atoms from trapped ensembles with unknown number of atoms. The method employs stimulated adiabatic passage to reversibly transfer a single atom to the Rydberg state which blocks subsequent Rydberg excitation of all the other atoms within the ensemble. This triggers the excitation of Rydberg blockaded atoms to short lived intermediate states and their subsequent decay to untrapped states. Using an auxiliary microwave field to carefully engineer the dissipation, we obtain a nearly deterministic single-atom source. Our method is applicable to small atomic ensembles in individual microtraps and in lattice arrays.