Over the past decade, our understanding of advanced pretreatments for cellulosic biofuels has grown exponentially. Using a host of analytical techniques, researchers have explored the fate of the plant cell wall during pretreatment and as a research community we have improved our understanding of the fundamental macro and nano-scale effects of pretreatment that influence the recalcitrance of biomass for biological deconstruction. Finally, these studies have shown that recalcitrance is a multi-structural effect involving, to varying degrees.