The fluorine redistribution during partial solid-phase-epitaxial-regrowth at 650 °C of a preamorphized Si substrate implanted by F was investigated by atom probe tomography (APT), transmission electron microscopy, and secondary ions mass spectrometry. Three-dimensional spatial distribution of F obtained by APT provides a direct observation of F-rich clusters with a diameter of less than 1.5 nm. Density variation compatible with cavities and F-rich molecular ions in correspondence of clusters are in accordance with cavities filled by SiF4 molecules. Their presence only in crystalline Si while they are not revealed by statistical analysis in amorphous suggests that they form at the amorphous/crystal interface.