This paper presents the results of atomic force microscopy and Raman spectroscopy studies of the effect of high-temperature annealing on the height/depth parameters of silicon areas modified by a focused ion beam. It is shown that the focused ion beam treatment with 5 beam passes leads to swelling of the surface of the modified silicon areas. It was found that the depth of the focused ion beam modified area is different after annealing at 600 and 800 °C. An increase in the number of passes in both cases led to an increase in the depth of the focused ion beam modified areas. The results of studies of Raman spectroscopy showed that with an increase in the number of passes, a decrease in the crystallinity of silicon occurs. It is also shown that annealing of such regions leads to the restoration of crystallinity upon annealing at 600 °C and almost complete restoration of crystallinity at 800 °C.