In this work we numerically investigated the decrease of low temperature thermal conductance of cylindrical Silicon nanofibers with periodical and almost periodical corrugation on the boundary. We used 1D and 3D finite element models to study scattering of low frequency acoustic phonons from the corrugation. By assuming weak deformation and high enough cross-sectional symmetry it was found that 1D models yield a sufficiently good approximation and could be used in the calculation of thermal conductance for long nanofibers. Landauer 1D formalism was applied for the calculation of the thermal conductance of several long axially symmetric and elliptical fibers. Without significantly hindering the structural strength of the fiber we found boundary shapes which decrease the thermal conductance by each mainly contributing phonon down to 10% of the universal quantum on temperature range 0.1–1K. We concluded that the similar drop in total thermal conductance could be obtained by combining these designs in series.