Microbial utilization of lignocellulose from plant cell walls is integral to carbon cycling on Earth. Correspondingly, secreted enzymes that initiate lignocellulose depolymerization serve a crucial step in the bioconversion of lignocellulosic biomass to fuels and chemicals. Genome and metagenome sequencing efforts that span the past decade reveal the diversity of enzymes that have evolved to transform lignocellulose from wood, herbaceous plants and grasses. Nevertheless, there are relatively few examples where ‘omic’ technologies have identified novel enzyme activities or combinations thereof that dramatically improve the economics of lignocellulose bioprocessing and utilization. A likely factor contributing to the discrepancy between sequence-based enzyme discovery and enzyme application is the common practice to screen enzyme candidates based on activity measurements using soluble model compounds. In this context, the development and application of imaging, physicochemical, and spectromicroscopic techniques that allow direct assessment of enzyme action on relevant lignocellulosic substrates is reviewed.