This paper discusses a method to watermark a 3D shape model defined as a set of unoriented points. Our approach is to perform frequency domain analysis of the shape of the 3D point set for watermarking. Our method applies the mesh-spectral analysis technique proposed by Zachi Karni, et al. to the point set model for frequency domain shape analysis. As the technique requires connectivity of vertices for the analysis, our method generates a non-manifold mesh from the point set and uses its connectivity for the analysis. The watermarks embedded by using the method can be detected, to some extent, after such attacks as cropping, (simulated) simplification, similarity transformation, and additive random noise applied on the watermarked point set model.