The design of mass exchanger networks (MENs) has drawn increasing attention in recent years, mainly because of attractiveness in pollution prevention and materials recovery. The integration of an MEN, however, will make a plant structurally more complicated. The process streams in the plant will be more heavily interacted. The interactions may be detrimental to stable process operation and effective waste reduction when severe entering disturbances propagate throughout the plant. Such a structural inferiority must be prevented in process design. The process structural superiority can be evaluated through process modelling. In the present work, a unique modelling methodology is developed to characterize disturbance propagation and predict the worst situations to occur in a plant when an MEN is integrated. In the methodology, a unified model structure is introduced to model mass separating agent-based separators, splitters, mixers, and a system composed of them. The model is simple and computationally efficient. It can be used to evaluate process alternatives and to select the most desirable one with maximum structural disturbance rejection in the early stages of process design.