We report the generation of complex toroidal nanoscale vortices in nanochannel flows, through the employment of patterned surface patches with contrasting wettability characteristics. Through extensive molecular-dynamics simulations, we further delineate that complicated interactions between the wettability gradient-driven vortex structures and surface roughness-influenced flow features may give rise to interesting patterns in the flow field. We also establish the orientation specificities of these nanoscale vortices, and demonstrate that the surface roughness effects may potentially act to alter the flow rotationalities realized out of modulated surface patterning effects to a considerable extent, which may have interesting consequences toward designing nanoscale mixing elements.