New trends such as mass customization have appeared, where production volumes are flexible, customers require One of a Kind production, and product variety is large. To accomplish these demands, there is a necessity of flexible enterprise operations and reconfigurable manufacturing systems. Enterprise models, integration frameworks, collaborative systems and flexible/reconfigurable manufacturing systems allow facing such challenges. This paper presents a methodology aiming to support the design, creation and implementation of sustainable, smart and sensing manufacturing systems. S 3 Enterprise (Sensing, Smart and Sustainable) Reference Model has been developed and used to create such systems. The S 3 Enterprise Reference Model uses a methodology based on action-research concept to pursue understanding and facilitating its implementation in Small and Medium Enterprises. The reference model is instantiated to define a Collaborative Networked Organization that is able to manufacture customized products. Finally, a case study is presented to demonstrate the usage and application of the methodology.