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Small angle neutron scattering (SANS) was used to study the structure of Avicel (FD100) microcrystalline cellulose during enzymatic digestion. Digestions were performed in either of two modes: a static, quiescent mode or a dynamic mode using a stirred suspension recycled through a flow cell. The scattering pattern for as-received Avicel in D₂O buffer is comprised of a low Q power law region resulting from the surface fractal character of the microcrystalline fibers and a high Q roll-off due to scattering from water-filled nanopores with radii ∼20 Å. For digestions in the dynamic mode the high Q roll-off decreased in magnitude within ∼1 h after addition of enzymes, whereas in the static digestions no change was observed in the high Q roll-off, even after 60 h. These results indicate that only with significant agitation does enzyme digestion affect the structure of the nanopores.