With the use of X-ray Standing Waves (XSW) and Atomic Force Microscopy (AFM), we have studied the structure and morphology of CaF2 films (thickness range 3-15 Angstrom) grown on Si(111) before and after modification by electron irradiation. The Ca monolayer of the as-grown CaF2 monolayer relaxes towards the Si substrate. The F bilayer embedding the Ca monolayer has bulk spacing. Low Energy (80-100 eV) Electron-Stimulated Desorption (ESD) of fluorine reduces mainly the occupation of the top F layer due to generation of surface color centers. The Ca layer is affected only marginally by the electron bombardment. For 15 Angstrom, CaF2 films the color centers nucleate and form Ca clusters embedded in the film. These clusters are removed under ambient conditions (pin hole formation). Inspection of the holes shows that the Ca clusters penetrate the entire CaF2 film.