We discuss the filtering of the vibrational states of a cold atom in an optical trap by chaining this trap with two empty ones and adiabatically controlling the tunneling. Matter-wave filtering is performed by selectively transferring the population of the highest populated vibrational state to the most distant trap while the population of the rest of the states remains in the initial trap. Analytical conditions for two-state filtering are derived and then applied to an arbitrary number of populated bound states. Realistic numerical simulations close to state-of-the-art experimental arrangements are performed by modeling the triple well with time-dependent Pöschl-Teller potentials. In addition to filtering of vibrational states, we discuss applications for quantum tomography of the initial population distribution and engineering of atomic Fock states that, eventually, could be used for tunneling-assisted evaporative cooling.