Focused ion beam (FIB) techniques have previously been shown to have applications in templating semiconductor nanostructure growth on Si. To assess crystalline quality in this method, or in other FIB-based nano-fabrication methods in Si, we assess in this work FIBimplantation damage in Si and subsequent recovery by annealing. Specifically, we study Si substrates implanted to 1 9 10 12 -5 9 10 15 ions cm -2 fluences of 30 kV Si 2? , Ge 2? and Ga ? incident normally at room temperature, covering a structural damage regime from almost no damage to amorphization. Raman spectroscopy with incident photons of wavelength 405 and 514 nm were used for probing structural damage in different depths in as-implanted and thermally annealed substrates. Annealing was performed for varying times at 730-900°C in ultra-high purity nitrogen ambient. Structural damage quantification was performed through measurements of peak height and position of the crystalline Si peak at 520 cm -1 . Our analysis shows that a structural damage parameter, D, (defined by subtracting from unity, the ratio of the height of the Si Raman peak in implanted/annealed samples to that for the Si peak in an unimplanted standard, such that D = 0.00 and D = 1.00 correspond to pristine single crystal and amorphous Si respectively) is 0.05 or less in all the Si and Ge implants after annealing to 900°C, 1800 s. However, D for the Ga implants is close to zero for Ga fluences up to 3 9 10 13 cm -2 but increases steadily to 0.19 for 5 9 10 15 Ga cm -2 under these annealing conditions. The underlying damage recovery mechanisms are discussed.