The contradictions of the historical data with the six-component model necessarily led to a refinement of the FCM model. The parts of the system under discussion are systems in themselves, and to investigate their deeper structure is essential to understanding the operation of the system. The subsystems form this way a system of systems”. Up-to-date engineering systems are often extremely complex, and they are usually composed of a multitude of interacting units, which are called subsystems. In areas where expert assessment is crucial, the process of expert participation in workshop form may ensure that the various opinions and interests are integrated into synergies and this way, sustainable solutions sought for can be found as a result of joint decision-making. Regional Waste Management Systems (RWMS) are also such complex systems where expert domain knowledge plays an important role, and which can always be subdivided into interconnected or separate subsystems and elements, where a number of factors has to be reconsidered and determined by an expert panel. These factors are usually complementary, in some cases conflicting or competing; but essentially the subsystems and subsystem elements influence each other and determine the overall operation of the system. In this Chapter, it will be shown how the workshop technique may result in a much more refined model, which may be the start of a model without contradictions and fully adequately simulating the real life system. The aim of the workshop designed and realised in the case study, described in the Chapter as a suitable method was to analyse the starting model and to construct an efficient new model of RWMSs, with more factors. The workshop method was applied in group sessions and plenary discussions. Expert teams were encouraged to develop a common, unified model of the system under investigation. This approach could hopefully help resolve the conflicts and disagreements in the previous model, and also, among certain experts’ opinions. In the case study, as a result, a more refined model was developed indeed, however, then the problem emerged, how to build up, how to deal with, and how to evaluate this rather complex model.