The paper deals with modelling of propagation medium for molecular communication, which consist of composite biological environments with multiple regions each with distinct diffusion properties for the understanding of the transport of information molecules. For this, we propose a generalized analytical approach for modelling a composite, diffusive, molecular communication channel for arbitrary placement of the transmitting and receiving nano-machines. Using this approach, we derive a generalised closed-form expression for the channel impulse response of a three dimensionally (3D) diffusive medium having multiple regions with an aim to act as a benchmark solution to validate simulations as well as to optimize the design of molecular communication systems. The pulse peak amplitude, pulse peak time and pulse width are derived to evaluate the system performance. In addition, a particle-based simulator for modelling a diffusive medium with multiple regions under three-dimensional diffusion is proposed and validated with the analytical results. It is shown that the channel impulse response and other communication metrics are significantly affected by the diffusion coefficients, regions thickness, properties of region interfaces as well as the positions of transmitter and receiver nano-machines with respect to the interfaces.