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This study addresses the complementary metal-oxide-semiconductor-compatible fabrication of vertically stacked Si/SiO2/Si nanopillars (NPs) with embedded Si nanodots (NDs) as key functional elements of a quantum-dot-based, gate-all-around single-electron transistor (SET) operating at room temperature. The main geometrical parameters of the NPs and NDs were deduced from SET device simulations using the nextnano++ program package. The basic concept for single silicon ND formation within a confined oxide volume was deduced from Monte-Carlo simulations of ion-beam mixing and SiOx phase separation. A process flow was developed and experimentally implemented by combining bottom-up (Si ND self-assembly) and top-down (ion-beam mixing, electron-beam lithography, reactive ion etching) technologies, fully satisfying process requirements of future 3D device architectures. The theoretically predicted self-assembly of a single Si ND via phase separation within a confined SiOx disc of < 500 nm³ volume was experimentally validated. This work describes in detail the optimization of conditions required for NP/ND formation, such as the oxide thickness, energy and fluence of ion-beam mixing, thermal budget for phase separation and parameters of reactive ion beam etching. Low-temperature plasma oxidation was used to further reduce NP diameter and for gate oxide fabrication whilst preserving the pre-existing NDs. The influence of critical dimension variability on the SET functionality and options to reduce such deviations are discussed. We finally demonstrate the reliable formation of Si quantum dots with diameters of less than 3 nm in the oxide layer of a stacked Si/SiO2/Si NP of 10 nm diameter, with tunnelling distances of about 1 nm between the Si ND and the neighboured Si regions forming drain and source of the SET.