We reviewed the new methods that can be used in the recycling of biomass, with regard to the modeling of enzymes and the new possibilities of their application. Progress has been made in the pretreatment of biomass, as well as in the diversity and application of the enzymes used, but based on molecular modeling, very little progress has been made in development. There is also minimal progress in modifying the enzymes used during biomass processing to adapt to environmental conditions. There are hardly any publications where molecular modeling techniques are used to modify, improve, and adapt enzymes to different environmental conditions. In our opinion, in addition to modern biochemical, enzymatic, and biotechnological methods, enzyme modeling would help in the targeted design and modification of enzymes used in biomass processing.