Mapping and visualization of structural changes due to the modification of wood would increase the understanding of chemical modification processes and facilitate optimization of the process parameters. The 2D and 3D microstructure of acetylated and furfurylated softwood and hardwood were visualized using X-ray computed tomography and some anatomical features were investigated such as total porosity, cell wall thickness and maximum opening of tracheid lumens. The wetting properties of chemically modified samples were related to the microstructural properties. Significant changes in the wood structure were observed for furfurylated sapwood samples mainly indicated by a change in tracheid shape and filling of tracheids by furan polymer, whereas no microstructural changes were noted for acetylated samples. Furfurylation significantly decreased the porosity of the sample in both earlywood and latewood regions; whereas for acetylated samples the total porosity of modified and unmodified samples was rather similar. This is in line with results of wetting showing that furfurylation reduced both swelling and capillary uptake in contrast to acetylation which reduced mostly swelling.