Mechanical metamaterials are designed to exhibit enhanced properties not found in natural materials or to bolster the properties of existing materials. The theoretical foundations for tuning the mechanical properties have been established, including topological states, controllable buckling behavior, and quasi-two-dimensional mechanical metamaterials with structures containing vacancies. However, the fabrication and experimental procedures to study these structures at the microscale have not been developed yet and the three-dimensional (3D) architectures examined to date are fairly limited. In this study, 3D mechanical metamaterial structures with select unit cells designed to have vacancies were fabricated by multi-photon lithography, having as the principal objective to control (localize) failure and increase the strain energy capacity of the structure. The metamaterial structure from which all the current designs originate is the octet-truss structure, one of the most widely studied 3D metamaterials. The design of the structures was inspired by the role of vacancies in crystal lattices. Vacancies were introduced in the metamaterial structures to allow localized buckling of lattice members to occur in specific unit cells. The significant increase of the strain energy dissipated in these metamaterials is demonstrated by nanoindentation experiments and finite element results. Vacancy effects on the dynamic response of metamaterial structures are also examined in the light of modal analysis simulations. The findings of this study illustrate the importance of strategically placing vacancies in the microlattices of metamaterial structures to control the overall mechanical behavior and greatly increase strain energy dissipation.