In the last twenty years, many theoretical studies have shown that plasmonic structures have astonishing, unique, and interesting optical characteristics. As a direct consequence, many scientific and industrial applications tried to take advantages by plasmonic, leading also to substantial innovation in nanofabrication methods. As an example, the combination of plasmonic nanostructures with complementary metal-oxide-semiconductor (CMOS) optical sensors, capable of converting photons into electrical signals, raised a great interest, due to potentiality of extend the spectral responsivity of Silicon in a wider spectral region, from the ultra-violet (UV) up to the near infra-red (NIR). Unlike the fabrication of plasmonic nanostructures on an inert substrate, the production of plasmonic nanostructures on active sensors requires consideration of surface topography as well as the sensors' active behaviors. Therefore, the choice of the production technique is a delicate step and required further investigation. Ion Beam Lithography (IBL), which does not require a mask or photoresist since the focused ions are deposited directly on the material of interest, is one of the process methods for fabricating nanostructures that is compatible with CMOS technology. Direct patterning by IBL gives the nanostructures total flexibility in terms of shape and aspect ratio. On the other hand, direct patterning can cause ions implantation in the substrate, causing flaws and modifying the electrical behavior of the sensors. Thus, to fabricate of plasmonic nanostructures directly on top of a CMOS sensors is pivotal to tune the IBL process parameters, such as beam energy and current, dose and ions species. In this paper, we demonstrate the optimization of Focused Ion Beam parameters by ion-solids interaction simulations and the preliminary results of direct patterning metallic nanostructures on a Si-based photodiode without damaging the active area and therefore, with an unmodified characteristic IV curve.