Accurate registration between medical images and patient anatomy is crucial for surgical navigation systems in minimally invasive surgeries. This study introduces a novel deep learning-based refinement step to enhance the accuracy of surface registration without disrupting established workflows. The proposed method integrates a machine learning model between conventional coarse registration and ICP fine registration. A deep-learning model was trained using simulated anatomical landmarks with introduced localization errors. The model architecture features global feature-based learning, an iterative prediction structure, and independent processing of rotational and translational components. Validation with silicon-masked head phantoms and CT imaging compared the proposed method to both conventional registration and a recent deep-learning approach. The results demonstrated significant improvements in target registration error (TRE) across different facial regions and depths. The average TRE for the proposed method (1.58 ± 0.52 mm) was significantly lower than that of the conventional (2.37 ± 1.14 mm) and previous deep-learning (2.29 ± 0.95 mm) approaches (p < 0.01). The method showed a consistent performance across various facial regions and enhanced registration accuracy for deeper areas. This advancement could significantly enhance precision and safety in minimally invasive surgical procedures.