Batch production is typical for engineering enterprises connected with aeronautical engineering manufacturing. One of its main problems is the need to periodically change the production pattern which arises as a result of the instability of the products range, changes in volume of series, moral and physical wear of technological equipment. Such a change is carried out in the course of reconstruction and technical re-equipment in order to improve the efficiency of material flows.The main characteristics of material flows are determined by a spatial component of a flexible manufacturing system pattern, set by the machine tools laying according to the organization of batch process. The bulk of the cost of final product manufacturing is associated with the arrangement of material flows. In order to reduce the total costs it is necessary to improve the pattern of production by establishing a technology-oriented machine tools laying. In this case, there is a need to develop scientific and methodological basis of restructuring the manufacturing process.One of the most effective approaches to the design of machine building plants with a batch type of manufacturing is the use of program-target method based on the methodology of choosing the best technological solutions.Modern methodology of batch technologies design is based on the system approach to the analysis and synthesis of the basic structure of the manufacturing processes, which allows to apply mathematical simulation.The orientation of each of the sites on the end result leads to a substantial reduction of manufacturing costs, which significantly simplifies solving problems of division and coordination of labor on the principles of self-organization and self-regulation.The proposed mathematical model of manufacturing costs optimization is designed in accordance with all the aforementioned principles. The problem being solved is multiobjective. That is why the mathematical model has several goal functions them requiring finding peak values and some of them requiring finding the bottom values.The model can be applied in organizing the aeronautical engineering manufacturing, which requires effective remounting during the change of product range thus ensuring the required flexibility of manufacturing.