A process modelling and simulation theoretical framework of general use for the study of continuous process industrial systems is introduced. The proposed process modelling methodology is based on Material Flow Networks and is implemented on a Process Simulation Modelling Tool developed for this purpose. The tool introduced can also serve the requirements arising for online use of the models as digital shadows of the physical systems, in the context of digital twinning the process industry. The implemented models in conjunction with tools from other scientific fields can be used for monitoring, root cause analysis, performance optimization, limitation and recovery of the behaviour of systems. An application example of the proposed methodology is provided and useful conclusions arise. Finally, extensions of the proposed method and potential challenges are discussed.