In this paper, the results of exploiting self-organized sub-micron polystyrene (PS) wrinkle patterns possessing random orientation, in preparation of a nickel stamp for hot embossing purposes, are presented. Self-organized patterns were prepared employing a method in which a stiff cross-linked capping layer on the topmost part of the soft polystyrene layer was created by using reactive ion etching (RIE) device with mild conditions and argon as a process gas, and the wrinkle formation was initiated thermally. Different surface patternings were obtained using silicon and stainless steel (SST) wafers as substrates. Prepared Ni-stamps were employed in hot embossing of polycarbonate (PC) and cyclo-olefin polymer (COP) films, using a nano-imprinting process. The replication quality of the self-organized wrinkle structures in PC and COP films was monitored by comparing the shape and dimensions of the original and final surface structures. The hot embossed sub-micron scale features, originally formed on stainless steel substrate, were found to have influence on the optical properties of the PC and COP films by lowering their reflectances.