We present a new methodology to fabricate surface structures based on coated magnetic particles and charged polymers. We control the surface architecture via a nanolithographic approach, Dip-Pen Nanolithography, which utilizes Atomic Force Microscopy (AFM) to delivery molecular "inks" on soid substrates. This process results in surfaces with a pre-programmed architecture composed of well-characterized negatively and postively charged polymeric regions. Charged magnetic particles coated via the Layer-by-Layer method can be assembled onto the pre-programmed surface blue-print using electrostatic interactions. The possibility of incorporating our templates in simple device strategies is currently being explored.