Biomass (e.g., plant biomass, animal biomass, and municipal waste biomass) or other materials are processed to produce useful intermediates and products, such as energy, fuels, foods or materials. For example, systems and methods are described that can be used to treat feedstock materials, such as cellulosic and/or lignocellulosic materials, in a vault in which the walls and optionally the ceiling include discrete units. Such vaults are re-configurable.