The article considers the issues of calculating and setting parameters of multilayer microbiological systems containing local concentrated discrete sources of temperature fields. As an object of research in the work, the considered multilayer, unlimited microbiological material subjected to local point thermal influence. The novelty of the author’s research is to take into account the specific features of the process of thermal action and the multilayer structure of microbiological material. The purpose of the research is to build physically justified computational mathematical models that describe the state of the research object, as well as to outline ways for the optimization process of a whole class of multilayer microbiological systems. The author has constructed a calculated mathematical model of the process of point thermal action on a multilayer unlimited microbiological material. It should be noted that a feature of the object of study is that its state is described by a boundary-value problem for a system of non-stationary, inhomogeneous differential heat equations (a system with distributed parameters). This specificity significantly complicates the process of constructing the appropriate mathematical models for optimizing multilayer microbiological systems, as well as their use to improve the quality of the biotechnological process of dividing (cutting, segmentation) microbiological material. In this regard, the author proposes to implement the procedure for solving a series of boundary value problems and ensuring an iterative process of searching for rational parameters of heat exposure on a specialized grid analog or hybrid model. This will allow at each iteration to significantly reduce the time it takes to solve a boundary value problem, which will make it possible to increase the accuracy of solving the entire problem of searching for parameters of the systems under consideration. Key words : mathematical models, optimization, boundary value problem, analog model, hybrid model