This research aims to develop an Image processing algorithm based on mathematics to pre-process, segment, and analyze the images obtained by the CT scan of Mangifera indica L. cv. mallika trunks, to identify the cavities created by the stem borer beetles. The methodology involves enhancing the CT images and identifying the cavities using a segmentation technique that utilizes Otsu’s thresholding and morphological operations. The findings indicate that a mathematical algorithm for segmentation was developed and applied to the CT images of the infected trunks with internal cavities created by the stem borer, which yielded more efficient and accurate results compared to an earlier study using X-ray images. It is noted that mango trees are an important segment of South Indian agri-food, and protecting them against infections caused by the stem borer, especially detecting them at an early stage, is vital. Although a few detection techniques are available, identification using imaging remains a novel idea that has not gained popularity.