We study the effect of polarized laser annealing on the crystalline structure of individual crystalline-amorphous core-shell silicon nanowires (NWs) using Raman spectroscopy. The crystalline fraction of the annealed spot increases dramatically from 0 to 0.93 with increasing incident laser power. We observe Raman lineshape narrowing and frequency hardening upon laser annealing due to the growth of the crystalline core, which is confirmed by high resolution transmission electron microscopy (HRTEM). The anti-Stokes:Stokes Raman intensity ratio is used to determine the local heating temperature caused by the intense focused laser, which exhibits a strong polarization dependence in Si NWs. The most efficient annealing occurs when the laser polarization is aligned along the axis of the NWs, which results in an amorphous-crystalline interface less than 0.5 νm in length. This paper demonstrates a new approach to control the crystal structure of NWs on the sub-micron length scale.