Confocal raman microscopy has been used to monitor the structural and chemical changes upon NaOH treatment of Miscanthus x giganteus, a potential energy crop and a model lignocellulosic material. Longitudinal and transversal-section images of the parenchyma cells in raw miscanthus samples reveal that lignin and cellulose are collocated in the cell wall and that a globular structure, composed predominantly of hemicellulose and lignin is associated with the interior cell wall. NaOH treatment results in the complete removal of lignin at long processing time but leaves the cellulose largely undisturbed as evidenced by the lack of conversion from type I to type II cellulose. Depth profiling images of partially processed (short exposure time) parenchyma cells reveal that lignin is removed preferentially from the interior surface of the cell wall as indicated by the anisotropic distribution of lignin and cellulose across the cell wall in partially processed samples. These spatially resolved chemical changes are important, because they illustrate how even simple pre-processing protocols can develop complex molecular profiles by differential rates of attack on the major components of the cell wall. (C) 2009 Elsevier Ltd. All rights reserved.