The aim of molecular communication (MC) is to develop communication systems for biochemical information interchange among nano devices. While there have been research efforts to model, design and analyze various MC network and devices, a lot still have to be done before we can develop and deploy such systems. Following the traditional physical layered architecture of communication networks, this paper presents design initiatives, open research issues and proffer suggestion towards modeling and designing diffusion-based MC devices. Specifically, we present biologically inspired modular theoretical design approach to modeling and designing MC devices. We also discussed various issues that should be considered in developing an accurate system-theoretic model of an MC system.