Pancreatic diseases are difficult to treat with high doses of radiation, as they often present both periodic and aperiodic deformations. Nevertheless, we expect that these difficulties can be overcome, and treatment results may be improved with the practical use of a device that can capture 2-D slices of organs during irradiation. However, since only a few 2-D slices can be taken, the 3-D motion needs to be estimated from partially observed information. In this study, we propose a physics-based framework for estimating the 3-D motion of organs, regardless of periodicity, from motion information obtained by 2-D slices in one or more directions and a regression model that estimates the accuracy of the proposed framework to select the optimal slice. Using information obtained by slice-to-slice registration and setting the surrounding organs as boundaries, the framework drives the physical models for estimating 3-D motion. The R2 score of the proposed regression model was greater than 0.9, and the RMSE was 0.357 mm. The mean errors were mm using an axial slice and mm using concurrent axial, sagittal, and coronal slices. Our results suggest that the proposed framework is comparable to volume-to-volume registration and is feasible.