This paper describes a methodology to design layout and cross-sectional shape and size for beam-like reinforcement to improve eigenfrequency. In case of the optimization for a structure using beam model, the topology, the layout, the cross-sectional shape and the size must be decided as design variables. In addition, some variables must be determined simultaneously because they have effect each other. Previously, we presented the design method which a layout and a cross-sectional shape are designed considering each correlation with feedback loop. In this paper, we describe a new method which has been improved previous method. The improved point is to be able to consider to insert some reinforcements for base structure. The design method which refers to the deformation on main structure is applied to least weight structural design with eigenfrequency constraint. In order to confirm a validity of proposal method, it is applied to design the reinforcement for three-dimensional beam structure. We have obtained the layout and the size of reinforcement for vibration proof.