It is well-known that surface plasmon generated near fields of suitably irradiated metal nano-structures can induce a patterning in an azobenzene-modified photosensitive polymer film placed on top. The change in the topography usually follows closely and permanently the underlying near field intensity pattern. With this approach, one can achieve a multitude of morphologies by additionally changing light intensity, polarization and the kind of metal used for nano-structuring. In this paper, we demonstrate that below a critical value of the polymer film thickness, the receding polymer material induces a change in refractive index of the glass–metal–polymer system, modifying the near field intensity distribution and causing a back-reaction on the flow of polymer material. This has a profound influence on the smallest size of topographical features that can be imprinted into the polymer.