The continuing trend for producing novel micro- and nanostructured devices and components in a broad range of materials is a major motivating factor driving the research in the micro- and nanomanufacturing sector toward developing innovative process chains. Some of such chains enable the serial production of micro- and nanostructured parts in polymer material by combining innovatively and optimizing simultaneously master making and replication technologies. For producing features at the nanoscale, the master making processes that are currently commonly employed rely on complex lithography-based pattern transfers and/or on beam-based direct write processes. Unfortunately, the required equipment to perform these techniques are often capital intensive and necessitate particular operating temperatures or vacuum conditions. At the same time, during the development phase of new or improved nanotechnology-enabled products, it is beneficial to produce rapidly polymer prototypes to test the functionality of components with nanoscale features. Thus, the technologies currently available for nanostructuring replication masters do not comply with the low cost requirements typically associated with the production of small batches of components for prototyping purposes. As a result, this could restrict the successful development of products with functional features at the nanoscale. In this research, a new process chain is presented for the fabrication of nanostructured components in polymer that relies on a simple and cost-effective master making technology. In particular, atomic force microscopy scratching is employed as an alternative technique for nanostructuring replication masters for microinjection molding. The conducted experimental study demonstrated the potential of this approach for small and medium series production of nanostructured devices in thermoplastic materials. In addition, the effects of different scratching parameters on the achievable surface roughness and depth of the patterned structures were analyzed by employing the design of experiments approach.