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. S3 Enterprise (Sensing, Smart and Sustainable) Reference Model has been developed and used to create such systems. The S3 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.