Methods and systems are described for processing cellulosic and lignocellulosic materials and useful intermediates and products, such as energy and fuels. For example, irradiating methods and systems are described to aid in the processing of the cellulosic and lignocellulosic materials. The electron beam accelerator has multiple windows foils and these foils are cooled with cooling gas. In one configuration a secondary foil is integral to the electron beam accelerator and in another configuration the secondary foil is part of the enclosure for the biomass conveying system.