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Nanoparticles of metals and semiconductors are promising for the implementation of a variety of photonic and electronic devices with superior performances and new functionalities. However, their successful implementation has been limited due to the lack of appropriate fabrication processes that are suitable for volume manufacturing. The current techniques for the fabrication of nanoparticles either are solution based, thus requiring complex surface passivation, or have severe constraints over the choice of particle size and material. We have developed an ultrahigh vacuum system for the implementation of a complex nanosystem that is flexible and compatible with the silicon integrated circuit process, thus making it suitable for volume manufacturing. The system also allows the fabrication of Ohmic contacts and isolation dielectrics in an integrated manner, which is a requirement for most electronic and photonic devices. We have demonstrated the power and the flexibility of this new system for the manufacturing of nanoscale devices by implementing a variety of structures incorporating nanoparticles. Descriptions of this new fabrication system together with experimental results are presented in this article. The system explains the method of size-selected deposition of nanoparticles of any metallic, semiconducting, and (or) insulating materials on any substrate, which is very important in fabricating useful nanoparticle-based devices. It has also been shown that at elevated substrate temperature, a selective deposition of the nanoparticles is observed near the grain-boundary regions. However, in these natural systems, there will always be low and favorable energy states present away from the grain-boundary regions, leading to the undesirable deposition of nanoparticles in the far-grain-boundary regions, too.