In image-guided radiation therapy, extracting features from medical point cloud is the key technique for multimodality registration. This novel framework, denoted Control Point Net (CPN), provides an alternative to the common applications of manually designed keypoint descriptors for coarse point cloud registration. The CPN directly consumes a point cloud, divides it into equally spaced 3D voxels and transforms the points within each voxel into a unified feature representation through voxel feature encoding (VFE) layer. Then all volumetric representations are aggregated by Weighted Extraction Layer which selectively extracts features and synthesize into global descriptors and coordinates of control points. Utilizing global descriptors instead of local features allows the available geometrical data to be better exploited to improve the robustness and precision. Specifically, CPN unifies feature extraction and clustering into a single network, omitting time-consuming feature matching procedure. The algorithm is tested on point cloud datasets generated from CT images. Experiments and comparisons with the state-of-the-art descriptors demonstrate that CPN is highly discriminative, efficient, and robust to noise and density changes.