The current state of a plstroyeniye of computing process in the information and measuring and operating systems (IMOS) of the flexible automated productions (FAP) is considered. The mathematical model of optimization of computing process in the top contour of IMOS of FAP is offered. Application of a method of branches and borders for the solution of problems of optimization of computing process, and also the theory of a duality for an assessment of limits of the decision and definition of an order of branching of variables in IMOS of FAP is described. Features of application of a gradient method of Errou-Gurvits for an assessment of limits of the decision in a method of branches and borders and results of experimental check of the developed mathematical models of optimization of vychmslitelny process are presented to IMOS of FAP. Methodical recommendations about use of mathematical apparatus of optimization of computing process in IMOS of FAP are made.