Modern thermoelectric devices incline toward inexpensive, environmentally friendly, and CMOS-compatible materials, such as silicon. To improve the thermoelectric performance of silicon, researchers try to decrease its thermal conductivity using various nanostructuring methods. However, most of these methods have limited efficiency because they are costly and damaging for the internal structure of silicon. Here, we propose a cost-effective, large-area, and maskless nanofabrication method that creates external nanocones on the silicon surface while preserving its interior. Our experiments show that these nanocones reduce the thermal conductivity of thin silicon membranes by more than 40%. Using a modified Callaway–Holland model, we study how the thermal conductivity is affected by various phonon scattering processes in the 4–295 K temperature range. We conclude that the nanocones generate additional surface scattering, which causes the thermal conductivity reduction. The proposed nanocones and their simple fabrication method are promising for the planar thermoelectric devices based on silicon.