AbstractLignocellulosic composite in corn stover is a candidate biofuel feedstock of substantial abundance and sustainability. Its utilization is hampered by resistance of constituent cellulose fibrils to deconstruction. Here we use multi-scale studies of pretreated corn stover to elucidate the molecular mechanism of deconstruction and investigate the basis of recalcitrance. Dilute acid pretreatment has modest impact on fibrillar bundles at 0.1 micron length scales while leading to significant disorientation of individual fibrils. It disintegrates many fibrils into monomeric cellulose chains or small side-by-side aggregates. Residual crystalline fibrils lose amorphous surface material, change twist and where still cross-linked, coil around one another. Yields from enzymatic digestion are largely due to hydrolysis of individual cellulose chains and fragments generated during pretreatments. Fibrils that remain intact after pretreatment display substantial resistance to enzymatic digestion. Optimization of yield will require strategies that maximize generation of fragments and minimize preservation of intact cellulosic fibrils.