The perfluoroacyl derivatives (pentafluoropropionylamides and heptafluorobutrylamides) of the primary and secondary regioisomeric amines, related to the controlled drug substance 3,4-methylenedioxymethamphetamine, are prepared and evaluated in GC-MS studies. These derivatives show excellent resolution on nonpolar stationary phases, such as RTX-1 and RTX-5, with elution order differences from those of the underivatized amines. The mass spectra for these derivatives are significantly individualized, and the resulting unique fragment ions allow for specific side-chain identification. The individualization is the result of fragmentation of the alkyl carbon-nitrogen bond, yielding hydrocarbon fragments and other unique ions. The heptafluoro butrylamides derivatives offer more fragment ions for molecular individualization among these regioisomeric substances.