sanjai2006:
I suspect that the odor is due to the presence of mercaptans and, if so, then it can be removed. However, before one can say what method should be used, more information is needed. Are you asking about a continuous stream of naphtha in a refinery ... or are you asking about a fixed volume in a tank or in other containers?
If you are talking about a continuous stream, then I suggest one of the Merox processes. See
http://en.citizendium.org/wiki/Merox and, in particular, the version for treating jet fuel, kerosene or naphthas.
If you are talking about a fixed volume in a tank or other container, then I suggest a simple wash or scrub with an aqueous solution of caustic (about 15 Baume sodium hydroxide).