Knowledge regarding the stifle ligament attachment sites in the canine stifle is crucial for relevant biomechanical studies and for pre-operative planning of the patient-specific, anatomical repair of ligament deficiency. The study aimed to establish deformable shape templates (DST) of the femur and tibia with embedding footprints of cranial and caudal cruciate ligament and lateral and medial collateral ligaments and to validate a shape transform procedure on the DST in obtaining the stifle ligament footprint locations. Fifty-four CT-based bone surface models of the femur and tibia were used to build respective statistical bone shape models (SSMs). The stifle ligament information was recruited from CT scans of 19 hindlimb specimens with radio-opaque marking on the ligament footprints. The averaged ligament footprint contours integrated with the corresponding SSM define the DST of the bones. The subject-specific ligament footprints were estimated in a leave-one-out cross-validation framework, in which the DST was transformed to achieve the shape-matching with the bone surface of the left-out sample and thereafter generate the corresponding footprint contours. The results showed that the Euclidean distances between the estimated and the reference footprint centroids were below 1.81 mm and 2.19 mm in the femoral and tibial sites, respectively. While the proposed method was shown to yield accurate estimations of cruciate ligament footprint locations, its applications in dogs with vast differences in body conformation were yet evaluated. Nonetheless, the shape transforms on the DST provides an alternative way to estimate the 3D footprint locations of the stifle ligaments in vivo.