Electrokinetic forces play an increasingly dominant role in micro-size domain. In the present work we describe a microfabrication process based on the combination of electrokinetic forces and electropolymerization of pyrrole. The described electrokinetic micromanufacturing technique allows for reliable and scalable integration of organic, inorganic, and biological materials into various microstructures. Computational modelling has been carried out to predict the effect of electrokinetic phenomena on the fabrication process. Additionally, experimental work has been carried out to verify the predictions of our model. It is expected that the electrokinetic micromanufacturing will provide a new important pathway for bridging the gap between nano-features and microstructures to allow batch processing of microelectrodes patterned with aligned nanotubes, other nano-particulates or entrapped biocells.