Phonons in low-dimensional structures with feature sizes on the order of the phonon wavelength may be coherently scattered by the boundary. This may give rise to a new regime of heat conduction, which can impact thermal energy transport and conversion. Traditional methods used to investigate phonon transport in one-dimensional structures suffer from uncertainty due to contact resistance, defects, and limited control over sample dimensions. We have developed a new batch-fabrication technique for suspended microdevices with integrated silicon nanowires from silicon-on-insulator (SOI) wafers. The nanowires are defect-free and have extremely high aspect ratios (length/critical dimension >2000). The nanowire dimensions (length and critical dimension) can be precisely controlled during fabrication. With these novel devices, phonon transport in silicon nanowires is systematically investigated. The room temperature thermal conductivity of nanowires with critical width around 80 nm is about 20 W/(m K) and much lower than that in smooth VLS wires. This suggests that the surface morphology of the structures has a significant effect on the thermal conductivity, but this phenomenon is not currently understood. This fabrication technique can also be used for thermal transport investigation in a wide-range of low-dimensional structures.