In this study, an experiment was conducted on hoop pine (Araucaria cunninghamii), which is 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 with a diameter of 39 cm and a height of 57 cm, and an 800 MHz Ground Penetrating Radar (GPR) antenna were used to determine the minimum image resolution and the size of the holes in the wood. GPR images of the timber were subjected to a filtering process to obtain characteristic reflection curves of the damage to the timber. Curves with clear waveforms were observed in the GPR profiles of eccentric holes with a diameter of 4 cm. Profiles of the damage were obtained and profile images with the trunk radius at the centre were transformed into polar coordinate images. From these polar coordinate images, the location, size and diameter of the eccentric holes in the wood were identified, and the reflection curves were characterised by waveforms and irregular fluctuations. The risk levels of tree trunks were determined on the basis of their t/R (minimum normal wall thickness of the cross-section of the trunk/radius of the trunk) values and hole area ratios. A comparison between the GPR-based results and the actual diameters of the holes revealed that the filtered GPR profiles could be used for the efficient and accurate assessment of damage to hoop pine timber (average error rate ≤ 4%).