Abstract In this paper we introduce a versatile tool for the controlled growth and alignment of copper-silicide nanocrystals. The method takes advantage of a unique self-organization phenomenon denoted as laser-induced periodic surface structures (LIPSS). Copper films (3 ± 0.2 nm) are sputter-deposited onto single crystal silicon (100) substrates with a thin oxide layer (4 ± 0.2 nm), and subsequently exposed to linearly polarized nanosecond laser pulses (τ ≈ 6 ns) at a central wavelength of 532 nm. The irradiation triggers dewetting of the Cu film and simultaneous formation of periodic Cu nanowires (LIPSS), which partially penetrate the oxide layer to the Si substrate. These LIPSS act as nucleation centers for the growth of Cu-Si crystals during thermal processing at 500 °C under forming gas 95/5 atmosphere. Exemplified by our model system Cu/SiO2/Si, LIPSS are demonstrated to facilitate the diffusion reaction between Cu and underlying Si. Moreover, adjustment of the laser polarization allows us to precisely control the nanocrystal alignment with respect to the LIPSS orientation. Potential applications and conceivable alternatives of this process are discussed.