We present a technique to control the spatial state of a small cloud of interacting particles at low temperatures with almost perfect fidelity using spatial adiabatic passage. To achieve this, the resonant trap energies of the system are engineered in such a way that a single, well-defined eigenstate connects the initial and desired states and is isolated from the rest of the spectrum. We apply this procedure to the task of separating a small pre-defined number of particles (up to 10) from an initial cloud and show that it can be implemented in radio-frequency traps using experimentally realistic parameters.