OBJECTIVE: Implant removal is a common method to quantify the level of osseointegration in small animal studies. Due to small implant sizes, precise alignment in removal experiments is crucial to obtain accurate and reproducible results. This study proposes a novel approach using photon counting detector computed tomography (PCD-CT) data and additive manufacturing to improve implant alignment. METHODS: A simplified finite element model was designed to investigate the effect of implant misalignment in removal tests. Additionally, the geometry of 43 rat tibiae was assessed utilizing PCD-CT scans, and subsequently specimen-specific positioning fixtures were designed and manufactured using computer-aided design and tabletop 3D printers. The accuracy and precision of the specimen alignment within the fixtures were assessed both visually (current state of the art) and through projectional radiography in both cranial-caudal (CC) and anterior-posterior (AP) projections to quantify true misalignment. RESULTS: Finite element analysis demonstrated that stresses and displacements are sensitive to misalignment, potentially leading to substantial inaccuracies in the implant removal measurements. Statistical analysis of visual assessments revealed poor to moderate inter- and intra-operator variability (0.336 ≤ ICC ≤ 0.625) and low correlation with true misalignment (0.024 ≤ R CONCLUSION: The proposed specimen fixation and alignment, which relies on clinical imaging data and inexpensive 3D printers, offers a cost- and time-effective alternative to visual assessments, which could considerably improve the accuracy and precision in osseointegration assessment.