In this paper we present the prototype of a decision support system for logical layout design of machining systems. The approach and developed decision support system are focused on systems which are used in the mass production of a unique product or a family of similar products. In these lines, the machining operations are realized on working positions equipped by standard modular spindle heads. The part transportation from a working position to the next one is synchronized. The spindle heads selected and their layout define the system productivity and the final cost. The paper present a novel approach and depicts mathematical and decision-aid methods developed and implemented in the software tool for optimization of each design (or reconfiguration) stage of such a line, in particular, a method for finding the optimal logical layout.