We utilize molecular dynamics simulations and show opposing roles of surface on dissipation in nanostructures. While the surface defects always aid in the entropy generation process, the scattering of phonons from rough surfaces can suppress Akhiezer damping. For the case of a silicon (2 Â 1) reconstructed surface, the former dominates and Q À1 (Q is the quality factor) is found to increase with the decrease in size. However, different scaling trends are observed in the case of a hydrogen (H) terminated silicon surface with no defects and dimers. Particularly, in the case of a H-terminated silicon, if the resonator is operated with a frequency X such that Xs ph < 1, where s ph is the phonon relaxation time and Q À1 is found to decrease with the decrease in size. The opposite scaling is observed for Xs ph > 1. A simplified model, based on two phonon groups (with positive and negative Gr€ uneisen parameters), is considered to explain the observed trend. We show that the equilibration time between the two mode groups decreases with the decrease in size for the H-terminated structure. We also study the scaling of Q À1 factor with frequency for these cases.