Despite intensive research activities in the field of laser-induced periodic surface structures (LIPSS), the large-area nanostructuring of glasses is still a challenging problem, which is mainly caused by the strongly non-linear absorption of the laser radiation by the dielectric material. Therefore, most investigations are limited to single-spot experiments on different types of glasses. Here, we report the homogeneous generation of LIPSS on large-area surfaces of fused silica using thin gold layers and a fs-laser with a wavelength λ = 1025 nm, a pulse duration τ = 300 fs, and a repetition frequency f rep = 100 kHz as radiation source. For this purpose, single-spot experiments are performed to study the LIPSS formation process as a function of laser parameters and gold layer thickness. Based on these results, the generation of large-area homogenous LIPSS pattern was investigated by unidirectional scanning of the fs-laser beam across the sample surface using different line spacing. The nanostructures are characterized by a spatial period of about 360 nm and a modulation depth of around 160 nm. Chemical surface analysis by Raman spectroscopy confirms a complete ablation of the gold film by the fs-laser irradiation. The characterization of the functional properties shows an increased transmission of the nanostructured samples accompanied by a noticeable change in the wetting properties, which can be additionally modified within a wide range by silanization. The presented approach enables the reproducible LIPSS-based laser direct-writing of sub-wavelength nanostructures on glasses and thus provides a versatile and flexible tool for novel applications in the fields of optics, microfluidics, and biomaterials.