We present a coherent filtering scheme which dramatically reduces the site occupation number defects for atoms in an optical lattice by transferring a chosen number of atoms to a different internal state via adiabatic passage. With the addition of superlattices it is possible to engineer states with a specific number of atoms per site (atomic crystals); which are required for quantum computation and the realization of models from condensed matter physics; including doping and spatial patterns. The same techniques can be used to measure two-body spatial correlation functions.