Interfacing devices with cells and tissues requires new nanoscale tools that are both flexible and electrically active. We demonstrate the use of PEDOT:PSS conducting polymer nanowires for the local control of protein concentration in water and biological media. We use fluorescence microscopy to compare the localization of serum albumin in response to electric fields generated by narrow (760 nm) and wide (1.5 μm) nanowires. We show that proteins in deionized water can be manipulated over a surprisingly large micron length scale and that this distance is a function of nanowire diameter. In addition, white noise can be introduced during the electrochemical synthesis of the nanowire to induce branches into the nanowire allowing a single device to control multiple nanowires. An analysis of growth speed and current density suggests that branching is due to the Mullins-Sekerka instability, ultimately controlled by the roughness of the nanowire surface. These small, flexible, conductive, and biologically compatible PEDOT:PSS nanowires provide a new tool for the electrical control of biological systems.