Precise pedicle screw placement is crucial in spine surgery, where minor inaccuracies can result in significant complications. Despite introducing robot-assisted navigation systems to aid surgeons, accommodating the spine's non-rigid movements (due to patient movement or interactions with the surgeon) often necessitates repeated intraoperative imaging, leading to increased radiation exposure. To address this challenge, we propose a novel method that utilizes the functional map (FM) framework to transfer drilling trajectories from preoperative CT scans to partially observed and noisy spine models. Specifically, the FM correspondences enhance the registration quality of pre-operative and perioperative 3D spine model data, even in the presence of non-rigid deformations. Through comprehensive simulations, we assess the method's effectiveness across various cases of complex deformations using a spine model consisting of five lumbar vertebrae obtained through CT scans. Validation involves evaluating registration errors in translation and rotation and verifying the clinical validity of transferred drilling trajectories. The results demonstrate the method's efficiency in transferring drilling trajectories onto noisy, partially observed, and deformed spine models.