This paper reports the practical experiences made with extending the Value Stream Mapping (VSM) approach to the comprehensive design of a lean manufacturing system for the series production of sheet metal cable tray systems. The use of VSM for analyzing the production of repetitive units has proven to be successful in different industries. It is based on a classification of all products into product families and creates one current and future state map for each product family. This approach and the related guidelines for future state optimization are very helpful but not sufficient for a comprehensive manufacturing system (re) design, because the relation between product families value streams, the overall material flow optimization, as well as the segmentation and layout of factory remains unclear. Thus, the purpose of this paper is to develop a design procedure based on the investigation of an industrial case that allows the integrated optimization of the single value streams, their compilation in material-flow optimized production segments, and finally the (re) design of production logistics and factory layout. The findings of this research are limited due to the focused nature of a case study based research. However, the obtained results encourage assuming its transferability to similar problems.