Superconducting Nb thin films have been nanostructured by means of a femtosecond UV laser. Laser induced periodic surface structures (LIPSS) with lateral modulation of and depth smaller than amplitude ( from crest to trough) are obtained for optimized laser scanning conditions over the film surface, i.e. power, frequency, scanning speed and polarization. This provides a fast and scalable procedure of surface control at the nanoscale. In thin films, control over the kinetics of the LIPSS formation process has been crucial. Untreated and laser-patterned samples have been characterized by electron and atomic force microscopy as well as by local and global magnetometry. The superconducting properties reveal anisotropic behavior in accordance with the observed topography. The imprinted LIPSS define channels for anisotropic current flow and flux penetration. At low temperatures, magnetic flux avalanches are promoted by the increased critical current density, though flux tends to be channeled along the LIPSS. In general, directional flux penetration is observed, being a useful feature in fluxonic devices. Scalability allows us to pattern areas of the order of cm /min.