The insoluble, ordered nature of cellulose in biomass represents a significant challenge for cellulases. Enzymes acting on cellulose have the challenges of first associating with and then disrupting the crystal packing of a highly structured substrate followed by directing a single-polymer chain into the active site tunnel where hydrolysis occurs in a stepwise (processive) fashion.  Enzyme processivity is influenced not only by the characteristics of the enzyme but by the nature of the substrate itself.  Computational Molecular Dynamic (MD) simulations coupled with mutational analysis and advanced biomass imaging techniques are providing a new understanding of the relationships between pretreatment chemistry and cellobiohydrolase action.  An overview of NREL’s efforts to develop a better understanding of the mechanisms of cellulase enzyme action at the molecular level through protein structure/function studies using advanced computer models, mutational analysis, and high-resolution imaging techniques will be presented.