Lignocellulosic biofuels has been considered as a sustainable and renewable resource for alternative energy.  However, the major challenge in the widespread adoption of biofuels is that biomass is intrinsically recalcitrant for its enzymatic conversion into sugar. Targeted lignin modification in bioenergy crops could potentially improve conversion efficiency of lignocellulosic biomass to biofuels. Wild-type and lignin-down-regulated alfalfa lines are imaged using coherent Raman Microscopy (CRM). The 1600 cm-1 Raman mode from lignin aromatic ring and 1100 cm-1 from cellulose are used in  to specifically represent the lignin and carbonhydrate signal in the plant cell walls. The label-free mapping of both cellulose and lignin renders their distributions on the cell walls. The effects of lignin modification on overall cell wall structure and carbohaydrate content distribution are discussed.