This work is conducted within the framework of the INFN QUANTEP (QUAntum Technologies Experimental Platform) experiment, an initiative aimed at developing a shared experimental platform for the advanced study of optical quantum technologies based on silicon photonics. The project pursues four primary strategic objectives: the design of silicon photonic circuits for quantum computing, the engineering of integrated single-photon sources, the development of integrated single-photon detectors operating at room temperature, and the application of quantum nanomaterials for the realization of integrated devices for polarization control. Specifically, the research presented herein focuses on two crucial aspects for the success of the experiment, adopting a dual-methodological approach. First, specific chip fabrication processes were optimized and completed using dual-beam instrumentation. Leveraging the expertise acquired in Focused Ion Beam (FIB) technology, platinum-assisted deposition was performed to create intra-chip electrical contacts. This technique proved instrumental in effectively operating on complex topologies, such as etched or non-planar areas, which are challenging to process using conventional fabrication techniques. Simultaneously, extensive use was made of FIB technology for the deposition and deterministic positioning of nanostructures on the chip, a key procedure to ensure experimental functionality and enable the modulation of the input optical signal polarization. To achieve this goal, an ad hoc experimental protocol was developed to synergistically integrate different techniques: Electron Beam Lithography (EBL) and subsequent drop-casting, combined with the use of nano-manipulators integrated within the FIB system. The employment of these tools enabled not only the cleaning of the substrate from unwanted residues resulting from the drop-casting process but also the controlled deposition of various nanowires in the vicinity of the waveguide with high spatial precision. This paper details the complete sequence of fabrication steps and the operational strategies implemented to achieve the deterministic positioning of the nanostructures.