We report on an atmospheric pressure plasma (APP) treatment of fused silica and its related surface and near-surface effects. Such treatment was performed in order to improve laser micro-structuring of fused silica by a plasma-induced modification of the glass boundary layer. In this context, an APP jet applying a hydrogenous process gas was used. By the plasma treatment, the transmission of the investigated glass samples was significantly decreased. Further, a decrease in the superficial index of refraction of approx. 3.66 % at a wavelength of 636.7 nm was detected ellipsometrically. By surface energy measurements, a decrease of the surface polarity of 30.23 % was identified. These determined modifications confirm a reduction of silicon dioxide to UV-absorbing silicon suboxide as already reported in previous work. Further, a change in reflexion by maximum 0.26 % was detected which is explained by the superposition of constructive and destructive interferences due to a surface wrinkling. With the aid of atomic force microscopy, an increase of the surface root mean squared roughness by a factor of approx. 19 was determined. It was found that both the surface energy and the strength of the fused silica surface were reduced by the plasma treatment. Even though such treatment led to a clustering of carbonaceous contaminants, a surface-cleaning effect was confirmed by secondary ion mass spectroscopy and energy-dispersive X-ray spectroscopy. The increase in UV-absorption allows enhanced laser ablation results as shown in previous work.