The paper is dedicated to proposed modelling approach for supply networks. The original structure of network systems can be modelled as complex adaptive systems and use agent-oriented simulation to demonstrate origin. The structure is clarified by expert opinion with use of DEMATEL method. The suitability of supply networks can be measured by multiple objectives, such as economic, environmental, social, and others. Traditional concepts of optimality focus on valuation of already given systems. We propose to use a methodology for optimal system design. As a methodology of optimal system design can be employed De Novo Multi-objective Linear Programming for reshaping feasible sets in linear systems.