A pulse of matter waves may dramatically change its shape when traversing an absorbing barrier with time-dependent transparency. Here we show that this effect can be utilized for controlled manipulation of spatially-localized quantum states. In particular, in the context of atom-optics experiments, we explicitly demonstrate how the proposed approach can be used to generate spatially shifted, split, squeezed and cooled atomic wave packets. We expect our work to be useful in devising new interference experiments with atoms and molecules and, more generally, to enable new ways of coherent control of matter waves.