Focused ion beam-secondary ion mass spectrometry (FIB-SIMS) with 20 nm spatial resolution has been used to analyze amorphous fluorinated carbon thin films, deposited by plasma assisted chemical vapor deposition (PACVD), at micro- to nano-scale. Mass spectra and ion imaging of film surface were acquired and the presence and distribution of contaminants were investigated. Surface images show the secondary ion distribution for F−, CH−, CF−. A change in size and topology of fluorine-rich areas is correlated with film hardness and with microstructure transition from diamond-like to polymer-like, as indicated by infrared and Raman spectroscopies. Based on the surface distributions of CF− and CH− and on the vibrational spectroscopy results, a mechanism of fluorine substitution for hydrogen and an attempt to explain the film structure and microstructure is proposed.