How to measure corrosion rate of an iron nail in salt water?
There is an ASTM standard(G01) that gives detailed descriptions of cleaning procedure for corrosion measurements.

For iron and iron oxide, the recommended way is to leave the sample in a cleaning solution(e.g a dilute acid solution), followed by a light brushing repeatedly until the weight stabilizes. 

You could also try sonication in a solvent to see if that helps. 

In any case, to make sure you are not losing significant amounts of the base metal, you should repeat the cleaning procedure on some uncorroded control sample. This will help you dial in the proper procedure for your samples.