Paper-based microfluidic systems are of great interest for cheap, disposable point-of-care diagnostic devices, especially for the use in the developing countries. The development of reliable and cost-effective fabrication methods is therefore of great importance. We present two novel methods and experimental setups for the area-selective creation of hydrophilic channels and hydrophobic barriers utilizing atmospheric-pressure microplasmas based on dielectric barrier discharges within the pores of the paper substrate. One approach is based on a local plasma etching process which is able to remove a hydrophobic coating from the paper fibers, while a second, alternative method uses patterned plasma polymerization to deposit a hydrophobic coating on the fiber structure. Both methods utilize microstructured electrodes to shape the plasma discharge volume to allow the fabrication of microfluidic structures in the substrate. We report on the influence of various processing parameters on the fabrication process and compare the minimal structure dimensions obtained so far and maximum wicking distances achieved. Both fabrication methods led to promising results with structure dimensions of around 400 µm, but the plasma etching process turned out to be superior due to lower cost, faster processing, and better structure edge definition.