We present here the observation of self-organized nanostructures on atmospheric microplasma exposed surfaces. In particular, we present the formation of self-aligned Mo-oxide nanoparticles, as well as the production of self-organized carbon-based connections between silicon nanocrystal micrograins and between Ag nanoparticles. The strong electromagnetic fields that are present at the processing surface play an important role in the self-organization process. This result represents an interesting phenomenon and suggests possible routes to promote and exploit self-organization for the production of nanostructured materials. (C) 2007 American Institute of Physics.