Claying should get rid of any surface contaminants. Either you are not claying properly (see Junkman2008's paint care threads on this site such as
Junkman's "How to Completely Repair Your Paint Damage - The Videos!) or the filings are embedded in the paint.
RustX is a great product but it is rather harsh so follow the directions and, as others have mentioned, be careful what it gets on.