We have developed a method for fabricating polymer microstructures based on electric field induced self assembly and pattern formation. A dielectric fluid placed in between to conductive plates experiences a force in an applied electric field gradient across the plates, which can induce a diffusive surface instability and self construction of the fluid surface. This process is exploited for the fabrication of self assembled polymer microstructures as well as replicated patterns through the use of pre-patterned plates or electrodes. We have used silicon wafers and transparent ITO (Indium-Tin Oxide) coated quartz substrates to fabricate the capacitor structures. The bottom silicon plate is spin coated with a 100-200 nm thick polystyrene film. The ITO substrate was placed over the polymer surface at a distance to leave a thin air gap using spacers. For directed pattern transfer, patterned ITO substrates were used. The capacitor setup was heated above the glass transition temperature of the polymer and a voltage was applied across the plates (50-150 Volts), which induces electric fields on the order of 107–108 V/m. The capacitor structure was quenched to observe the structures using optical microscopy and atomic force microscopy. The method described can be used to fabricate a variety of structures in the micron and nanometer scales including bio-fluidic MEMS, polymer optoelectronic devices and patterned templates for nanolithography.