We have performed refining process of yttrium (Y) by removal of fluorine (F) residually existing in commercial Y metal. It was demonstrated that combination of conventional plasma arc melting and mechanical surface polishing is a powerful method for removal of F, the residual concentration of which was traced by energy dispersive X-ray spectroscopy of as processed material and X-ray photoemission spectroscopy of as deposited films, which were grown using the processed material as a deposition source. As a result, the concentration of F in our purified material was assessed to be smaller than 3.5 wt ppm, which is approximately 1.3% of the initial F concentration present in the unpurified material (260 wt ppm).