An experiment was conducted on hoop pine (Araucaria cunninghamii), a common tree species in Taiwan. Holes with diameters of 4, 5, 7, 10, 12, and 14 cm were drilled in dry hoop pine timber (diameter: 39 cm, height: 57 cm). A ground penetrating radar (GPR) antenna set to 800 MHz was used to determine the minimum image resolution and the size of the holes within the timber. GPR reflections of the timber were subjected to a filtering process to enable identification of the characteristics of curves of the images of the damage. Curves with clear waveforms were observed in the reflections of the GPR profiles of eccentric holes with diameters of 4 cm. Profiles of the damage were obtained, and the profile images with the trunk radius considered the center were transformed into polar coordinate–based images. From these images, the location, size, and diameter of the eccentric holes within the timber could be identified, and the curves representing the reflections were characterized by waveforms and irregular fluctuations. The risk levels of the trunks were determined on the basis of their t/R values and hole area ratios. A comparison between the GPR-based results and the actual diameters of the holes revealed that the GPR profiles processed through filtering could be used for efficient and accurate assessment of the damage done to hoop pine timber (average error rate ≤ 4%).