A new method for covalently binding side-chains to the surface of solution based conducting polymer nanostructures is introduced in this paper. Modification of the structures is achieved by convenient reflux in the presence of a nucleophile, and post-functionalization purification is subsequently carried out by centrifugation. The entire process is easily scalable and hence suitable for bulk production of functionalized nanomaterials. In particular we focus on the modification of polyaniline nanofibres which can be synthesized by interfacial polymerization. Mercaptoundecanoic acid side-chains are attached to the polymer nanostructures, with the intrinsic nano-morphology of the material being maintained during the process. The modified PAni nanofibres provide a template for the attachment of other specific functional groups which could be used to target a particular species.