We report on a protocol to achieve full control of the polarization in a nanofiber. The protocol relies on monitoring the light scattered out from a nanofiber by means of two optical systems with 45°camera angle difference. We study the disturbance of the nanofiber refractive index on the radiation of embedded scatterers, and we propose an explanation for the observed reduced scattering contrast of the nanofiber. Thanks to this approach, we demonstrate an accuracy of the polarization control larger than 95%.