Ultrafast laser ablation of metal surfaces is a common physical process used to generate periodic surface structures with tuneable multifunctionality for various applications in science and technology. In this work, the formation of femtosecond laser-induced periodic surface structures (LIPSS) is investigated with 50 kHz repetition rate laser of 40 fs pulse duration and a central wavelength (λw=1030nm) along with its second (λ2w=515nm) and third (λ3w=343nm) harmonic components. The variation in the LIPSS periodicity is demonstrated by changing the wavelength of the ablating laser pulses. LIPSS with periodicity ~ 0.85 μm at the fundamental ablating pulses, ~0.42 μm periodicity at the second harmonic, and ~0.35 μm periodicity at the third harmonic generation were observed. We apply the third harmonic radiation generated in air filament with minimal temporal delay with respect to the fundamental driving pulses to structure nickel surfaces at ambient conditions. Our presented approach demonstrates the potential for generating very fine LIPSS on materials’ surfaces using the efficient high-order harmonics of an infrared fundamental laser beam.