There is a need to understand how cellulose structural properties impact productive cellulase-cellulose interactions toward solving the mechanisms of the heterogeneous reaction. We coupled biochemical studies of cellulose hydrolysis by a purified Trichoderma reesei Cel7A (TrCel7A) cellobiohydrolase with atomic force microscopy (AFM) to study the impact of the cellulolytic activity on the fibrillar structure of cellulose. Bacterial cellulose (BC) fibrils were hydrolyzed by TrCel7A then immobilized by hydrophobic interactions on glass for AFM imaging. Commonly used methods to culture and isolate cellulose fibrils resulted in significant oxidation of the reducing-ends but minimal oxidation along the fibrils. We observed extensive fibrillation of BC fibrils to ∼3 nm microfibrils during the course of hydrolysis by TrCel7A, leaving thinned un-fibrillated recalcitrant fibrils at >80% hydrolysis extents. Additionally, this remaining fraction appeared to be segmented along the fibril length.