The properties of organic heterostructures with mixed layers made of arylenevinylene-based polymer donor and non-fullerene perylene diimide acceptor, deposited using Matrix Assisted Pulsed Laser Evaporation on flat Al and nano-patterned Al electrodes, were investigated. The Al layer electrode deposited on the 2D array of cylindrical nanostructures with a periodicity of 1.1 µm, developed in a polymeric layer using UV-Nanoimprint Lithography, is characterized by an inflorescence-like morphology. The effect of the nanostructuring on the optical and electrical properties was studied by comparison with those of the heterostructures based on a mixed layer with fullerene derivative acceptor. The low roughness of the mixed layer deposited on flat Al was associated with high reflectance. The nano-patterning, which was preserved in the mixed layer, determining the light trapping by multiple scattering, correlated with the high roughness and led to lower reflectance. A decrease was also revealed in photoluminescence emission both at UV and Vis excitation of the mixed layer, with the non-fullerene acceptor deposited on nano-patterned Al. An injector contact behavior was highlighted for all Al/mixed layer/ITO heterostructures by I-V characteristics in dark. The current increased, independently of acceptor (fullerene or non-fullerene), in the heterostructures with nano-patterned Al electrodes for shorter conjugation length polymer donors.