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Nanostructured materials and nanolattices with high porosity can have novel optical and mechanical properties that are attractive for nanophotonic devices. One existing challenge is the integration of microstructures that can be used as waveguides or electrodes on such nanostructures without filling in the pores. This study investigates the fabrication of TiO2 microstructures on nanolattices using a stencil mask. In this approach, the nanostructures are planarized with a polymer film while the microstructures are patterned in a sequential shadow deposition step. Our results demonstrate the successful fabrication of a “dog-bone” microstructure with 400 μm length, 100 μm width, and 30–560 nm thicknesses on nanostructure with 390 and 500 nm period. The experimental results show that cracks can form in the microstructures, which can be attributed to residual stress and the thermal annealing cycle. A key finding is that the film cracks decrease as the TiO2 layer becomes thinner, highlighting an important relationship between grain size distribution and the film thickness. The mechanical stability of the underlying nanolattices also plays a key role, where interconnected architecture mitigated the crack formation when compared with isolated structures. The demonstrated fabrication process can lead to integrated waveguides and microelectrodes on nanolattices, which can find applications for next-generation photonic and electronic devices.