In this paper, we proposed a novel, simple and cost effective methodology to fabricate biocompatible, high charge density, highly scalable, three dimensional (3D) flexible microelectrode arrays (MEA). Existing methodologies for fabricating MEAs are very complex, expensive and predominantly of two dimensional geometries. The proposed MEA comprises an array of sharp pyramid shaped gold tips coated with Poly (3, 4-Ethylene Dioxy Thiophene) (PEDOT) using simple electro polymerization. The purpose of PEDOT is to increase the charge density/charge storage capacity manifold. Furthermore, the entire process of fabricating MEA utilizes a novel replica molding technique which involves development of single master mold on Silicon and replicating the same onto any flexible polymer. Thus the proposed process is highly scalable. © 2016 IEEE.