Time-of-flight secondary ion mass spectrometry (TOF-SIMS) is one of very few analytical techniques allowing sample chemical structure to be characterized in three-dimensional (3D) with nanometer resolution. Due to the excellent sensitivity in the order of ppm-ppb and capability of detecting all ionized elements and molecules, TOF-SIMS finds many applications for analyzing nanoparticle-containing systems and thin films used in microdevices for new energy applications, microelectronics, and biomedicine. However, one of the main drawbacks of this technique is potential mass interference between ions having the same or similar masses, which can lead to data misinterpretation. In this work, we present that this problem can be easily solved by delivering fluorine gas to a sample surface during TOF-SIMS analysis and we propose mechanisms driving this phenomenon. Our comprehensive studies, conducted on complex thin films made of highly mass-interfering elements, show that fluorine modifies the ionization process, leading to element-specific changes of ion yields (which can vary by several orders of magnitude), and affects the efficiency of metal hydride and oxide formation. In conjunction, these two effects can efficiently induce separation of mass interference, providing more representative TOF-SIMS data with respect to the sample composition and significant enhancement of chemical image resolution. Consequently, this can improve the chemical characterization of complex multilayers in nanoscale.