Highly oriented pyrolytic graphite samples were irradiated with C+ ions at 35 keV in a direction normal to the basal plane and subsequently annealed up to 1373 K. Substantial surface topography changes were observed at fluences of 5×1018 ions/m2 and higher using scanning electron and atomic force microscopies. Intricate networks of surface cracks and ridges developed after high dose implantation. A systematic study of the irradiation effects was conducted using Raman spectroscopy. Microstructural changes in irradiated regions were first detected at a dose of 1×1017 ions/m2 through the appearance of the Raman D-line at ∼1360 cm−1. The intensity of this line increases while that of the Raman G-line at 1580 cm−1 decreases as the irradiation dose is increased or the irradiation temperature is decreased. After irradiation at 280K to a fluence of 5×1019 ions/m2 or higher the first order spectrum exhibits one single line at a wavelength intermediate between the D- and G-lines. Damage recovery upon thermal annealing depends not only on the initial damage state but also on the annealing temperature sequence. Samples irradiated to a damage level where two distinct Raman peaks are no longer resolvable exhibited upon direct annealing at a high temperature two distinct Raman lines. By contrast, pre-annealing these highly irradiated specimens at lower temperatures produced less pronounced changes in the Raman spectra. Pre-annealing appears to stabilize damage structures that are more resistant to high-temperature annealing than those induced by irradiation.