Structure, morphology, and conductivity of SrZrO3 nanowires self-organized on rippled SrRuO3∕SrTiO3 surface templates by pulsed laser deposition are investigated by transmission electron microscopy and atomic force microscopy using dc-poled conductive tips. The responsible mechanism for the self-organized growth of fully-relaxed epitaxial SrZrO3 on the SrRuO3 ripple tops is identified as geometric shadowing induced by both the surface template morphology and the broadening of the angular distribution of the flux of incident particles. The latter process reflects the interactions between the deposition gaseous atmosphere (here molecular oxygen is at pressures ≈10−1 mbar) and the ejected plume of laser-ablated particles. The broadening, as estimated from the average scattering angle of the particles within incident flux measured in an artificial shadowing experiment, served as input to simulate numerically the morphological evolution of the resulting nanostructured system, wired SrZrO3/rippled SrRuO3∕SrTiO3.