Modeling and simulation of physiological processes deal with the challenges of multiscale models in which coupling is very high within and among scales. Information technology approaches together with related analytical and computational tools will help to deal with these challenges. Physiological Model Simulation, Integration and Modeling Framework, Phy-SIM, provides the modeling environment which will help to cultivate various approaches to deal with the inherent problem of multiscale modeling of physiological systems. In this paper, we present the modular design of Phy-SIM. The proposed layered design of Phy-SIM, separates structure from function in physiological processes advocating modular thinking in developing and integrating physiological models. Moreover, the ontology based architecture will improve the modeling process by the mechanisms to attach anatomical and physiological ontological information to the models. The ultimate aim of the proposed approaches is to enhance the physiological model development and integration processes by providing the tools and mechanisms in Phy-SIM.