Purpose The purpose of this study was to compare the accuracy of the planimetric methods on volume estimations by using cone beam computed tomography (CBCT). Materials and methods Thirty-one prepared intraosseous bone defects from thirteen bovine femur condyles were scanned with CBCT. The defect volumes were estimated by point counting (PC), manual segmentation (MS) and semiautomatic segmentation (SAS) methods at 0.3-mm section thickness without any intersection gap. The estimated volumes were compared with the results of the Archimedes' method. The planimetric methods were analyzed using a Friedman's two-way analysis of variance test. Results The estimated volumes of MS and SAS methods were compatible with the volumes of Archimedes' method (p = 0.768, p = 0.140, respectively), but the volumes from the PC method were not compatible with Archimedes' method (p < 0.001). Conclusion SAS was approximately 2.5 times faster than MS. Both MS and SAS are valid methods for volume estimation; however, SAS may be preferred due to its practicability.