We consider nanopatterning of dielectric substrates by harmonics of single powerful femtosecond pulses from a Ti:Sapphire laser. The nanopatterning is mediated by closely packed monolayers of polystyrene microspheres that act as microlenses at the surface. Observed modification of the material proceeds via ionization. By our theory, the second harmonic is more effective in multi-photon ionization and is better focused than the fundamental frequency which is effective in multiplying of the amount of free electrons via impact ionization. Experiments show that conversion of a part of the pulse energy into the second harmonic decreases the modification threshold and improves the localization of the structures. Optimization of the time offset between the harmonics could further improve the efficiency and quality of nanostructuring.