Bioinspired nanostructured antibacterial surfaces are among the most promising recent discoveries in nanotechnology to tackle microbial colonization of surfaces, especially with the growing challenge of antimicrobial resistance. Reactive ion etching (RIE) is one of the few nanofabrication techniques that has been demonstrated to be capable of generating biomimetic nanostructures on large substrates through a combination of physical and chemical etching. However, the physics behind the formation of these structures and their spatiotemporal evolution is poorly understood, primarily limited by the challenges associated with placing in situ characterization instruments inside the process chamber. The limited understanding in the field leads to poor reproducibility, constraining the widespread acceptance and application of this technique. This work describes maskless RIE of commercially pure titanium substrates using chlorine and fluorine plasma. It is demonstrated that the chamber condition plays a critical role toward determining the morphology of the nanostructures generated, and high aspect ratio (HAR) nanostructures can be generated reproducibly by following proper cleaning protocols involving fluorine plasma by scavenging the SiOCl species that accumulate in the chamber walls over time. Furthermore, the control of several process parameters to reproducibly fabricate various types of nanostructures such as nanoridges, nanopillars, and nanowires are demonstrated, along with insights into the underlying physical principles. HAR nanopillars are generated, and their bactericidal mechanism and efficiency are shown to be primarily dependent on their aspect ratio. This study provides insights to resolve the hitherto poorly understood events of fabrication of bioinspired nanostructures by RIE with important implications for reliably and reproducibly engineering biomaterial surfaces with bactericidal activity.