Layer-by-layer assembly of polyelectrolytes is a simple technique based on the self-assembly of polycations and polyanions mainly by electrostatic interactions, which has gained considerable scientific interest for its versatility of applications. Ease of fabrication process, inexpensive approach and use to coat surfaces with various geometries prompts the researchers to select this technique not only for the surface modification applications but also to study the processes which exploit the 3D matrix properties of polyelectrolyte multilayer films (PEMs). Recent advances have been made where PEMs coatings have been utilized for their bio-applications like drug delivery and in tissue engineering for modifying the biomaterial's surfaces. In the field of drug delivery and tissue engineering the location and availability of the constituent molecules is very important, which is defined by their ability to diffuse through the encapsulating material or reservoir. So the main objective of this thesis is to understand the transport of molecules in ultrathin Polyelectrolyte Multilayer Films in lateral as well as transverse direction to the substrate. To study this transport behaviour in PEMs, we have employed various strategies which can enhance or suppress the diffusivity across PEMs. Thus, understanding the diffusion at nanoscale resolution will lead us to design better host materials for loading of drugs and growth factors for various biomedical applications.