Polyelectrolyte multilayer (PEM) organic thin films with diameters ranging from 80 to 200 nm can be generated from dip-pen nanolithography (DPN) fabricated templates. Through the use of multi-pen AFM cantilever probes, parallel fabrication of PEM features with nanoscale resolution can be achieved. This demonstrates the versatility of the parallel DPN approach and its applicability to building nano-/microscale structures in conjunction with a layer-by-layer method.