Pressurized hot water extraction with a flow-through system was used to extract hemicelluloses and lignin from birch sawdust. The structure of the extraction residue was studied on various levels. Molecular mass distributions were determined with gel permeation chromatography and the crystal structure of cellulose was characterized using wide-angle X-ray scattering (WAXS). Information on the short-range order of cellulose microfibrils and on the nanoscale pore structure was obtained with small-angle X-ray scattering (SAXS), and the micrometre scale cellular morphology was imaged with X-ray microtomography. The pressurized hot water treatment was observed to increase the lateral width of cellulose crystallites, determined with WAXS, whereas a possible small decrease in the crystallinity of cellulose compared to native wood was detected. The molecular mass of cellulose remained at a relatively high level. According to the SAXS results, a tighter lateral association of cellulose microfibrils was observed in the extracted samples, which possibly led to opening of pores between bundles of microfibrils, as indicated by an increased specific surface area. A reduction in the thickness of the fibre cell walls was evidenced by X-ray microtomography.