Ensiling has been proposed as a method of feedstock storage for biorefineries. The traditional use of ensiling is to provide winter forage and to increase forage digestibility for livestock, but the potential effect of ensiling on feedstock bioconversion hasn't been fully examined. As part of a collaboration between INL and NREL to determine the effect of ensiling on biomass conversion, we have used microscopic imaging techniques to analyze the impact ensiling has on cell wall structure. We were able to assess mechanical, chemical, and biological disruption to the structure of ensiled corn stover cell walls. Also, we were able to detect microbial colonization and direct microbial interactions with cell walls. From a microscopic analysis perspective, the cell walls of ensiled corn stover appear to have been altered somewhat by ensiling. While there is not the extensive re-localization of cell wall matrix components as seen in dilute acid pretreated cell walls, the cell walls of ensiled materials do appear loosened compared to senesced, field-dried feedstock. Based on these structural parameters alone, we would anticipate that these materials should be at least as digestible as field-dried material.