Deposition of aligned forests of 1D nanoparticles (carbon nanotubes and MnO2 nanorods) on conductive, including flexible and transparent, substrates has been achieved at room temperature. The process, named high-voltage electrophoretic deposition (HVEPD), has been enabled by three key elements: high deposition voltage for alignment, low dispersion concentration of the nanoparticles to avoid aggregation, and simultaneous formation of a holding layer by electrodeposition. The effects of key parameters are investigated. The alignment on the vertical direction has been revealed by scanning electron microscopy of the samples, their superhydrophobicity, electrochemical performance, and capability to electrically connect two separated electrodes. Compared with their randomly oriented counterparts, the aligned nanoforests showed higher electrochemical capacitance, lower electrical resistance, and the capability to achieve superhydrophobicity, implicating their potential in a broad range of applications.