To unravel the effects of phonon confinement, the influence of size and morphology on the atomic vibrations is investigated in Sn nano islands and cluster-assembled films. Nuclear resonant inelastic X-ray scattering is used to probe the phonon density of states of the Sn nanostructures which show significant broadening of the features compared to bulk phonon behaviour. Supported by ab initio calculations, the broadening is attributed to phonon scattering and can be described within the damped harmonic oscillator model. Contrary to the expectations based on previous research, the appearance of high-energy modes above the cut-off energy is not observed. From the thermodynamic properties extracted from the phonon density of states, it was found that grain boundary Sn atoms are bound by weaker forces than bulk Sn atoms.