In this article, we present a design methodology for resonant structures exhibiting particular dynamic responses by combining an eigenfrequency matching approach and a harmonic analysis-informed eigenmode identification strategy. This systematic design methodology, based on topology optimization, introduces a novel computationally efficient approach for 3D dynamic problems requiring antiresonances at specific target frequencies subject to specific harmonic loads. The optimization’s objective function minimizes the error between target antiresonance frequencies and the actual structure’s antiresonance eigenfrequencies, while the harmonic analysis-informed identification strategy compares harmonic displacement responses against eigenvectors using a modal assurance criterion, therefore ensuring an accurate recognition and selection of appropriate antiresonance eigenmodes used during the optimization process. At the same time, this method effectively prevents well-known problems in topology optimization of eigenfrequencies such as localized eigenmodes in low-density regions, eigenmodes switching order, and repeated eigenfrequencies. Additionally, our proposed localized eigenmode identification approach completely removes the spurious eigenmodes from the optimization problem by analyzing the eigenvectors’ response in low-density regions compared to high-density regions. The topology optimization problem is formulated with a density-based parametrization and solved with a gradient-based sequential linear programming method, including material interpolation models and topological filters. Two case studies demonstrate that the proposed design methodology successfully generates antiresonances at the desired target frequency subject to different harmonic loads, design domain dimensions, mesh discretization, or material properties.