Combination of polymers with their excellent workability and long-term stability with inorganic nanomaterials exhibiting unique physic-chemical properties opens the way for preparation of nanocomposites with wide range of potential applications in electronic, environmental, medical and biomedical industry. Despite of testing of various metal nanostructures in biomedicine, the best results, particularly antibacterial effects, have been achieved with the silver-based ones. Silver nanowire arrays on the surface of polyethylene naphthalate (PEN), first modified by KrF excimer laser irradiation and then silver coated, were prepared. The laser fluence and angle of incidence of laser beam, were changed to achieve required sample surface morphology, which was controlled by AFM, SEM and FIB-SEM techniques. The surface properties of the samples in different phases of their preparation were characterized by XPS and UV-Vis. The influence of the surface morphology of the samples on their antibacterial effect was investigated by drop plate method using Gram-negative bacteria E. coil and Gram-positive S. epidermidis. The release of Ag ions into working medium was controlled by ICP-MS. The surface morphology of polymeric substrate was found to have a great influence on the resulting antibacterial effect of such silver/polymer composites.