A combination of lithography and thermoplastic forming allows us to fabricate honeycombs from bulk metallic glass (BMG) precisely and to manipulate its structure selectively. Characteristics of the honeycomb such as the ligament length, thickness, and radius of curvature at the joints of the cells are varied to determine how changes in these characteristics affect properties under uniaxial in-plane compression testing. It is found that the deformation behavior of BMG honeycombs can be controlled through microstructural design, from brittle to ductile, by changing the length to thickness ratio of the ligaments. The ability to absorb energy of BMG honeycombs exceeds honeycombs of most other materials due to the utilization of a size effect, which result in plasticity. Besides the usage for BMG honeycombs, the technique provides a general method to effectively characterize complex microstructural architectures and tailoring these architectures to the specifications of the material used.