Preoperative planning for high tibial, distal femoral, and tibial tubercle osteotomies has traditionally relied on cross-sectional two-dimensional (2D) images obtained from computed tomography (CT) scans. However, recent studies have underscored the potential advantages of three-dimensional (3D) reconstruction in preoperative planning. The present study aims to compare lower extremity alignment parameters obtained using 2D and 3D measurement techniques before peri-articular osteotomies used to treat patellofemoral disorders. All lower extremity osteotomies performed between 2022 and 2024 at our institution were retrospectively identified. Eligible patients received both 2D and 3D CT measurements prior to surgical intervention. For both imaging modalities, tibial tuberosity-trochlear groove (TT-TG), tibial torsion, and Caton-Deschamps (CD) index measurements were obtained. Paired t-tests were used to assess discrepancies between radiographic measurements obtained from 2D and 3D reconstruction. Statistical significance was defined as p ≤ 0.05. In total, 52 patients (66.0% female) with a mean age of 31.1 ± 9.0 years were identified. Median 2D and 3D measurements were similar for TT-TG distance (16.0 vs. 16.3 mm) and CD index (1.1 vs. 1.2), while median tibial torsion was greater on 2D compared with 3D imaging (27.0 degrees vs. 22.7 degrees). The average absolute difference between modalities were 3.1 mm for TT-TG distance (interquartile range [IQR]: 1.0–5.0), 5.6 degrees for tibial torsion (IQR: 1.0–7.5 degrees), and 0.16 for CD index (IQR: 0.05–0.22). Statistically significant differences in tibial torsion measurements highlight potential limitations of 2D CT measurements in capturing 3D complexity. These findings suggest that 3D preoperative planning leads to improved accuracy in postoperative multi-planar alignment goals. Further research is needed to evaluate the clinical implications of these differences and to refine imaging protocols for preoperative planning.