The development and efficient production of effective bioplastics is a hot topic, required to face up to the issue of the difficult disposal of plastics derived from oil. Among the different natural sources of bioplastics, starch is one of the most promising. However, for most applications, the proper mastering of the surface properties of bioplastic is necessary. We report about the surface modification of extruded corn starch films by means of cold plasma based on helium (He) and hexamethyldisiloxane (HMDSO). The differently treated surfaces were functionally characterized in wettability and water absorption. The nanoscale morphology was assessed by scanning electron microscopy and atomic force microscopy. The obtained images were analyzed by advanced figures describing both texture and amplitude parameters, including fractal behavior. The combined treatment (He/HMDSO) resulted in more homogeneous films with smaller, better-distributed grains compared to the case wherein He was not used. Despite the different morphologies observed, starch coated by HMDSO alone and by He/HMDSO presented similar hydrophobic character, with contact angles higher than 110°. Plasma treatment with HMDSO and He/HMDSO resulted in a significant reduction of absorbed water content without reduction of water vapor permeability. The nanotexture of the films did not present statistically significant differences, in terms of spatial complexities, dominant spatial frequencies, homogeneous void distribution, and surface percolation.