Conducting vertical nanopillar arrays can serve as three-dimensional nanostructured electrodes with improved performance for electrical recording and electrochemical sensing in bio-electronics applications. However, vertical nanopillar-array electrodes made of inorganic conducting materials by conventional nanofabrication approach still faces challenges in high manufacturing costs, poor scalability, and limited choice of carrier substrates. Here, we report a new type of conducting nanopillar arrays composed of multi-walled carbon nanotubes (MWCNTs) doped polymeric nanocomposites, which are manufactured over the wafer-scale on both rigid and flexible substrates by direct nanoimprinting of perfluoropolyether nanowell-array templates into uncured MWCNT/polymer mixtures. By controlling the MWCNT ratios and the annealing temperatures during the fabrication process, MWCNT/polymer nanopillar arrays can possess outstanding electrical properties with high DC conductivity (~4 S/m) and low AC electrochemical impedance (~104 Ω at 1000 Hz). Moreover, by electrochemical impedance spectroscopy (EIS) measurements and equivalent circuit modeling-analysis, we can decompose the overall impedance of MWCNT/polymer nanopillar arrays in the electrolyte into multiple bulk and interfacial circuit components, and thus can illustrate their different dependence on the MWCNT ratios and the annealing temperatures. In particular, we find that a proper annealing process can significantly reduce the anomalous ion diffusion impedance and improve the impedance properties of MWCNT/polymer nanopillars in the electrolyte.