The effect of phonon scattering by surface roughness on the thermal conductance in mesoscopic systems at low temperatures is calculated using full elasticity theory. The low frequency behavior of the scattering shows novel power law dependences arising from the unusual properties of the elastic modes. This leads to new predictions for the low temperature depression of the thermal conductance below the ideal universal value. Comparison with the data of Schwab et al. [Nature (London) 404, 974 (2000)] suggests that surface roughness on a scale of the width of the thermal pathway is important in the experiment. DOI: 10.1103/PhysRevLett.87.115502 PACS numbers: 63.22. +m, 63.50. +x, 68.65. -k Thermal transport in mesoscopic systems at low temperatures shows universal properties analogous to the quantized electrical conductance [1]. Theoretical analyses of phonon transport when the thermal wavelength becomes comparable to the dimensions of the thermal pathway predict a thermal conductance K that is independent of many of the details of the geometry and material properties [2], and a universal value for K͞T N 0 p 2 k 2 B ͞3h at low enough temperatures [3,4]. (Here N 0 is the number of modes with zero frequency at long wavelengths, equal to 4 for a single, free-standing elastic beam.) These predictions have since been connected to more general results on bounds on entropy transport at low temperatures [5] and to thermal transport by particles of arbitrary statistics [6]. The recent confirmation of the universal thermal conductance in tiny silicon nitride devices [7] is an experimental tour de force. Although verifying the predictions of a universal value of K͞T at low enough temperatures, the experiments showed values of K͞T that decrease as the temperature increases in the range of 0.08 to 0.2 K, before beginning to rise at higher temperatures as more vibrational modes that can carry the heat are excited.We [8] and others [9,10] have previously studied a simplified treatment of this problem using a scalar model for the elastic waves. However, elastic waves in confined geometries have many unusual features, such as modes with a quadratic dispersion relation v~k 2 at small wave numbers k and regions of anomalous dispersion dv͞dk , 0, that are not captured in this simple model and might be expected to have a strong influence on the low temperature transport.In this Letter we study the general problem of the scattering of phonons by rough surfaces for a rectangular cross-section elastic beam using three-dimensional elasticity theory. The scattering of the low frequency modes that contribute to the conductance at low temperatures depends on the detailed properties of the elastic modes, and we find novel power law dependences for the frequency dependence of the scattering off unstructured roughness that are not those anticipated by simple analogy with Rayleigh scattering. In turn this low frequency behavior yields a depression of K͞T at low temperatures with unexpected power laws, with a faster decrease of K͞T as the temp...