Apatites are phosphate minerals of a general formula Ca5(PO4)3(OH,Cl,F). They are are the principal constituent of teeth and bone (natural and synthetic); represent an important accessory minerals in volcano geological environment by means as a storage of elements such as halogens, sulphates, carbonates, Sr and REE; represent a packaging of radionuclides for nuclear waste, trapping heavy metals and finally are mostly used fertilizers. This work is focused on fluorapatite, the Fluorine-rich composition. As mentioned by several authors, SEM and EPMA analysis of F-apatites is complicated by the strong consequences of electron beam damages. This problem is particularly strong for the determination of fluorine concentration. Indeed a complex intensity variation is observed for the fluorine signal collected by the spectrometer; this variation mainly depends on two parameters: crystal orientation of the mineral grain and electron beam setup. Crystallographically-oriented Fluor-apatite were irradiated under the EPMA electron beam, using different setup (i.e. acceleration voltage, beam current, beam size) following the F, Ca and P WDS-variations signal. Beam damages were characterized by SEM and µ-Raman (including Raman-in-SEM).