Brands and products counterfeiting, and falsification are global problems for the development and distribution of high‐tech industrial and food products, which affect world economies. One way to solve these problems is to develop original packaging with protection elements and labeling against counterfeiting, which excludes the possibility of replication and forgery by printing or other methods. The most reliable way to protect packaging from counterfeiting is the use of new materials with unique optical properties and constantly updated technologies for packaging manufacturing and labeling. This paper proposes a new multi‐level technology for the design, manufacture and hidden labeling of polymer packaging made from several layers of transparent polymer films. The design and marking of the multilayer films are combined with perforation, thermal treatment and heat sealing of the package. The reliability of the proposed markings is based on the characterization of optical pleochroism effects in transparent multilayer polymer materials with shape memory. The thermomechanical and optical properties of films made of bulk thermoplastics (polypropylene, polystyrene, polyvinyl chloride and polyethylene) were characterized in polarized light. The modification and combination of these films provide a high color difference and sufficient contrast of hidden markings, allowing to identify genuine products by bar codes formed from shape memory films in sealing seams of flexible polymer packaging.