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Large-area nanostructuring of glasses using intense laser beams is a challenging task due to the material’s extreme non-linear absorption of laser energy. Precise optimization of the process parameters is essential for fabricating nanostructures with large-area coverage. In this study, we report the findings on creating high-spatial-frequency LIPSS (HSFL) on borosilicate glass through direct laser writing, using a femtosecond laser with a wavelength λ = 800 nm, pulse duration τ = 35 fs, and repetition frequency frep = 1 kHz. We measured the single-pulse ablation threshold and incubation factor of Borosilicate glasses to achieve high-precision control of the large-area surface structuring. Single-spot experiments indicated that, when there was higher fluence and a larger number of irradiated laser pulses, a melt formation inside the irradiated area limited the uniformity of LIPSS formation. Additionally, the orientation of the scan axis with the laser beam polarization was found to significantly influence the uniformity of LIPSS generated along the scan line, with more redeposition and melt formation when the scan axis was perpendicular to the laser beam polarization. For large-area processing, the borosilicate glass surface was scanned line-by-line by the laser beam, with a scan orientation parallel to the polarization of the laser. The optical characterization revealed that the transmittance and reflectance of the borosilicate glass decreased significantly after processing. Additionally, the surface’s wettability changed from hydrophilic to super-hydrophilic after processing. These chemical contamination-free and uniformly distributed structures have potential applications in optics, microfluidics, photovoltaics, and biomaterials.