This paper introduces a systematic deterministic framework for planning and the analysis of facility layouts aimed at manufacturing a variety of parts, being components of specific end products. The essence of the proposed approach lies in the decomposition of a traditional job-shop into layout modules of generic material flow patterns that inherently yields improved efficiency of the entire system. It entails the use of a relevant reasoning scheme based on production flow analysis and the method of hierarchical clustering of specified process routings for parts. The approach has been studied in the aspect of its application in an actual woodworking facility, dealing with fabrication of wooden toy sets. The respective workflows were subjected to the analysis in order to identify production bottlenecks using data derived from the real case study. As a result, the designated process layout alternatives have been evaluated in terms of assumed measures of the operational performance. An inseparable part of the research was exploring the capability for the optimum selection of a multi-part product mix, to be fabricated in defined time frames. In this regard, the usability as well as the computational efficacy of the integer linear programming modelling have been fully confirmed. The results gained show in particular that the suggested methodical scheme could be a useful tool in planning optimised manufacture of customised wood products of modular construction.