Plasmonic nanoholes are a kind of important building blocks for practical plasmonic applications due to their unique properties supporting extraordinary transmission and strong field enhancement. However, the reliable fabrication of plasmonic nanoholes with high-fidelity geometry, especially in thick metallic film, is still challenging with the current wet lift-off or focused-ion beam process. In this work, we demonstrate a process combining negative-tone electron-beam lithography, metal sputtering and flood ion-beam planarization to reliably fabricate plasmonic nanoholes. Compared to existing lift-off process, it has the advantages of 100% yield, uniform geometry and smooth structural edges. In contrast to focused-ion beam process, the current approach has apparently higher throughput and structural fidelity. Plasmonic nanoholes with different geometries, materials and sizes are reliably fabricated to demonstrate the advantages of this approach. The extraordinary transmission properties and their potential for refractive-index sensing are also demonstrated. This lithography-deposition-planarization strategy can also be extended to fabricate other optical structures such as optical metasurfaces and X-ray zone-plates.