Fuel storage instability reactions of middle distillate fuel are of interest to the Department of Defense. Unlike civilian fuel, military fuel can remain in storage tanks for one or more years. As fuel is drawn from these tanks, the tanks are subsequently topped off with more recently purchased fuel, and the mixed fuel is not compatible, resulting in sediment and sludge formation. Previous research has shown that certain polar organic nitrogen functional groups involved in instability reactions are difficult and expensive to remove completely during the refining process. Therefore, this study involved the removal of these compounds by four different filtering media. An unstable fuel was treated separately with activated clay, silica gel, amorphous carbon, and iron carbon nanotubes (FeCNT) and the composition of the extracts were analyzed by GC/MS. The results of this study show that some of the media were not only more effective, but selective in removing the organic nitrogen compounds.