Diffusion behavior of spin cast polymer thin films was studied in detail as a function of film thickness. Diffusion coefficients of water molecules in poly(methyl methacrylate) (PMMA) were found to decrease from 10-8 cm2/s in thick films to 10-13 cm2/s in ultra-thin films. In order to probe if there is a characteristic length scale set by the polymer chain size, the effect of PMMA molecular weights on this behavior was tested and deviation of diffusion coefficient from bulk was observed in all molecular weights of PMMA investigated. Diffusion coefficients in these films was also studied as a function of aging time at 25°C and was not found to change significantly over a time period of approximately four months. The impact of residual casting solvent in thick and thin films was studied and found to have no influence in the diffusion behavior. Positron Annihilation Lifetime Spectroscopy (PALs) was used to probe the free volume (FV) pocket size and its distribution within the film as a function of film thickness in PMMA. Decrease in FV pocket size was found to be one of the general underlying causes for such thickness dependent diffusion behavior observed in thin polymer films. In addition, Protracted Colored Noise Dynamics (PCND) that enables efficient sampling of phase space and faster relaxation of the systems compared to Molecular Dynamics (MD) was investigated for its extensibility to three dimensional systems and was found to be sensitive to initial conformation.