This paper considers the configuration of physical systems in a business to business environment (machine tool, aerospace equipment, cranes ...). In this kind of business, knowledge-based configuration software are frequently used when dealing with Assemble/Make-To-Order or (Configure-To-Order (CTO)) situations where the entire customer’s requirements can be fulfilled with standard systems. However, in Engineer-To-Order (ETO) situations where non-standard systems must be designed in order to fulfill the entire customers’ requirements, existing knowledge-based configuration software cannot be used. In fact, the configuration hypothesis state that all configured systems are assembled from standard sub-systems and components. The aim of this paper is therefore to investigate how the existing products/systems configuration hypothesis, problems’ definitions, and models can be modified or adapted in order to allow the use of configuration software in ETO situations. In this purpose, first, the main differences between standard and non-standard systems are analyzed. Then, six cases of systems configuration that differentiate CTO from ETO are identified and discussed. Finally, some Constraint Satisfaction Problems (CSP) based modeling extensions are proposed to allow the use of configuration software in these situations.