The size, distribution, and specific shape of ordered nanophotonic structures are crucial for their biomedical applications. Bottom‐up approaches such as self‐assembly, emulsification, and precipitation are commonly fabricated nanophotonic structures, which often lack control of nanophotonic structures morphologies and monodispersed sizes. On the contrary, top‐down nanofabrication techniques offer the advantages of high fidelity and high controllability and are employed in the fabrication of nanophotonic structures. This review focuses on top‐down nanofabrication techniques to fabricate ordered nanophotonic structures and their biomedical applications. Several top‐down approaches used in the semiconductor industry and other fields requiring micro‐ and nanopatterns are used, including electron beam lithography/ion beam lithography, photolithography, interference lithography, nanoimprint lithography, nanosphere lithography, nanotransfer lithography, and nano‐electrodeposition. Various current and emerging biomedical applications of the ordered nanophotonic structures are also covered: i) surface‐enhanced Raman scattering, ii) plasmonics, including surface plasmon resonance and localized surface plasmon resonance, and iii) fluorescence enhancement. Finally, a future perspective of nanophotonic structures fabricated by top‐down techniques in biomedical applications is also summarized.