Nowadays, many factories face changes on the global market and manufacturing is unpredictable. This fact creates a demand for developing new concepts of the factory which can represent a solution to these changes. This study presents a way for designing these new factory concepts, particularly a concept of the reconfigurable manufacturing lines. The methodology in this study uses characteristics of reconfigurable manufacturing systems for developing an algorithm for designing the basic factory layout. The methodology also combines classical math operations for designing the production layout with such approaches as simulation, cluster analysis, and LCS algorithm. This combination method with LCS algorithm and an entirely different approach to the design of the manufacturing line, has not yet been used. The accuracy of this methodology is then verified through the results of the complete algorithm containing these features. The main purpose of this study was to find new approaches to designing the reconfigurable factory layout. This article is presenting new ways that differ from the classical design method. The article suggests the new way is possible and the new systems also need new ways for designing and planning.