In this letter, we report a novel approach to selectively functionalize the surface of silicon nanowires located on silicon-based substrates. This method is based upon highly localized nanoscale Joule heating along silicon nanowires under an applied electrical bias. Numerical simulation shows that a high-temperature (>800 K) with a large thermal gradient can be achieved by applying an appropriate electrical bias across silicon nanowires. This localized heating effect can be utilized to selectively ablate a protective polymer layer from a region of the chosen silicon nanowire. The exposed surface, with proper postprocessing, becomes available for surface functionalization with chemical linker molecules, such as 3-mercaptopropyltrimethoxysilanes, while the surrounding area is still protected by the chemically inert polymer layer. This approach is successfully demonstrated on silicon nanowire arrays fabricated on SOI wafers and visualized by selective attachment of gold nanoparticles.