This paper presents a method for the design of manufacturing networks focused on the production of personalised goods. The method, which is implemented to a software tool, comprises of a mechanism for the generation and evaluation of manufacturing network alternative configurations. An exhaustive search and an intelligent search algorithm are used, for the identification of efficient configurations. Multiple conflicting user-defined criteria are used in the evaluation, including cost, time, CO2 emissions, energy consumption and quality. Discrete Event Simulation models of manufacturing networks are simulated for the calculation of performance indicators of flexibility, throughput and work-in-process, and are used for assessing the performance of centralised and decentralised networks. The results obtained through the exhaustive and intelligent search methods are compared. The applicability of the method is tested on a real-life industrial pilot case utilising data from an automotive manufacturer.