We present room temperature scanning tunneling microscopy (STM) investigations of well-aligned, polyaniline passivated, multiwall carbon nanotubes (MWCNT). STM topographic images show that nanotubes are partially covered with the conducting polymer. On atomically resolved scale we observed an array of caps with round shape that are separated by polyaniline. Differences in the electronic conduction between nanotubes and the polymer suggest that this method could be used to synthesize large-scale nanodevices.