A custom-built gas cluster ion source with energy up to 50 keV is constructed, and Ar, CO₂, N₂, and O₂ are used as the working gases. The clusters are formed by a metal supersonic conical nozzle with critical diameter in a range of 65–135 μm and a cone angle of 14°. The nozzle is powered in the pulsed mode, which improves the pumping conditions, and also makes it possible to increase the gas pressure in the stagnation zone to 15 atm and thereby obtain larger clusters. Based on the principle of ultrasonic expansion, gas cluster ions with an average size of 3000 atoms are obtained. The cluster beam current of 50 μA is obtained. The Ar cluster beam, which is less reactive, is used for treating surface, namely, surface smoothing and formation of self-assembled nanostructures. The Ar cluster bombardment perpendicular to the surface of the substrate is used to demonstrate the smoothing of the surface of Si wafers, Ti coating, and Au film. For the initial Si wafer, its root-mean-square (RMS) roughness of 1.92 nm decreases down to 0.5 nm after cluster beam treatment. The cleaning effect of the cluster beam is also observed very well. The one-dimensional (1D) isotropic power spectral density of the Si surface topography before and after smoothing are also discussed. The off-normal irradiation Ar cluster beam is also used to form self-assembled surface nanoripple arrays on the surface of flat ZnO single crystal substrates. The ripple formation is observed when the incident angle of the cluster beam is in a range of 30°–60°. The process of nanoripple fabrication is significantly governed by the cluster beam incident angle, energy and dose. The nano-ripples formed on the flat substrates remain eolian sand ripples and their formation starts at the incident angle of 30°. The most developed nanoripples are observed at the incident angle within a range of 45°–60°. The surface morphology and characteristic distribution of the nano-structures on the flat ZnO substrate are also analyzed by the two-dimensional (2D) power spectral density function. Next, Ar cluster beam is used for irradiating the ZnO nanorod arrays grown on the Si substrate. Due to various angles between the nanorod’s axis and the substrate normal, the conditions of the ripple formation on the nanorod facets are also realized. The dependence of wavelength on the accelerating voltage of the cluster ions and the dose are studied. Similar dependence of wavelength on accelerating voltage and dose are found for nanorods. Comparing with the flat ZnO surface, nanoripples on the ZnO nanorod faces at high irradiation doses demonstrate an ordering effect, and morphology of the ripples resembles that of more parallel steps rather than eolian ripples.