We outline an electrodeposition procedure from an emulsion to fabricate novel vertically aligned open and closed-pore microstructures of poly(N-(2-cyanoethyl)pyrrole) (PPyEtCN) at an electrode surface. Adsorbed toluene droplets were employed as soft templates to direct polymer growth. The microstructures developed only in the presence of both ClO4- and H2PO4- doping ions due to a slower rate of polymer propagation in this electrolyte. Two sonication methods (probe and bath) were used to form the emulsion, producing significantly different microstructure morphologies. Control over microtube diameter can be achieved by simply altering the emulsion sonication time or the amount of toluene added to form the emulsion. Electrochemical characterization indicated the PPyEtCN microtube morphology had an increased electrochemical response compared to its bulk counterpart. TEM analysis of individual closed-pore microtubes identified a hollow interior at the base within which the toluene droplet was encapsulated. This cavity may be used to entrap other compounds making these materials useful in a range of applications. The methodology was also applied to form microstructures of poly(3,4-ethylenedioxythiophene) and polypyrrole.