In this perspective, the state of the art in modeling of biomass processing to produce fuels and chemicals is reviewed, and the potential impact of modeling, along with the computational challenges, is presented. First, we discuss metal catalyzed chemistry, such as hydrogenation, hydrodeoxygenation, and reforming in vapor/solid reactions. Density functional theory (DFT) and microkinetic modeling of ethylene glycol and glycerol are reviewed and recent progress and challenges in modeling of unsaturated aldehydes and furans are discussed. A computational engine is presented that enables computer-based high throughput screening to derive performance maps and identify optimal catalysts. Condensed-phase processes are then covered with emphasis on solvent effects (e.g., solvation of biomass molecules, participation of solvent in the chemistry), thermodynamic properties, and separations. The conversion of fructose to 5-hydroxymethylfurfural (HMF) is taken as a prototype case of this class of processes. Finally, an outlook is provided.