This paper presents the process development towards a new generation of nanostructured thermoelectric generators for power harvesting from small temperature gradients by using a combination of traditional silicon microfabrication techniques, electroplating and submicron ion-track nanolithography. Polyimide nanotemplates with pore diameters ranging from 30 nm to 120 nm were fabricated. Preliminary results from the fabrication of poly(methyl methacrylate) (PMMA)-nanostructured templates are reported. Bi2Te3 nanowires (80 and 120 nm diameters) were electroplated into polyimide ion-track nanotemplates. Bi2Te3 nanowires of a R3 m structure, with preferential orientation in (1 1 0) crystallographic plans, were electroplated. The chemical composition of Bi2Te3 with nearly stoichiometric composition (Bi2.31Te3) was obtained. Homogeneity profiles of the chemical composition were obtained. A fine-grained observed microstructure (6–10 nm) and (1 1 0) crystalline orientation were obtained, which is extremely promising for improving the thermoelectric material properties. The thermoelectric properties of the Bi2Te3-electroplated thin films (Seebeck coefficient α) and electrical resistivity of the Bi2Te3 bundle nanowires were found to be −52 µV K−1 and ~14 MΩ cm, respectively. Polyimide (Kapton foil) and PMMA 950 photoresists were promising materials for the realization of a nanostructured thermoelectric generator on flexible and rigid substrates, respectively.