In this paper, we present a shape optimization method by using pyramid shape basis vectors for a natural frequency problem of plate and shell structures. The local embossed shape besides the global shape can be optimized by this method. The pyramid shape basis vectors are created using the small lattice domains so as to express the local shape variation in the normal direction on the surface, which is based on the concept of the shape function of the finite element method. The morphing technique is employed to vary the domain consisting of the several finite elements. A natural frequency set as the objective function is maximized tracking the mode under a volume constraint condition. The results for two examples show the validity of this method to optimize both the global shape and the local embossed shape of plate and shell structures for the natural frequency problem. In addition, the results of a stiffness problem of the same models are presented for comparison.