In this article, a multi-stage system analysis of a processing device using IR to Cocoon through systems thinking was carried out, analysing the elements of the hierarchical structure of the device and the processes that take place in each element. The elements of the IR device go deep into the device from top to bottom, and the input and output parameters are selected starting from the internal positions of the device. If we consider the biochemical processes occurring in the material at the lower levels of the hierarchy, the changes in the material to be processed, the heat and mass transfer processes in the elements at the top of the hierarchy, the resulting changes, are analysed by means of a multi-step structural analysis. Based on the results of the system analysis, mathematical equations are generated for each process from the links between input and output parameters from the lower stage to the upper stage, and on their basis mathematical models are formed to determine the optimum process conditions. On the basis of the mathematical models constructed, the optimum use of the treatment device through IR to the stage is selected