Annealing of thin Au films sputtered on polyimide (PI) and polyetheretherketone (PEEK) polymer substrates was carried out to study influence of substrate on surface morphology transformation and possible "dewetting", which was observed in the past on glass substrates. Thermal stability of substrates was studied by differential scanning calorimetry, PI substrate was found to be stable up to 400 degrees C, PEEK undergoes crystallization at circa 170 degrees C and melts at circa 320 degrees C. Therefore, annealing temperatures of 200 degrees C and 300 degrees C were chosen for PEEK and PI respectively. Surface morphology of the samples was studied by atomic force microscopy. Annealing of the PEEK substrate leads to significant changes of its surface structure, a rugged structure is formed. A sufficiently thin Au layer is then broken into islands, thicker layers however cover the substrate structure. Annealing of Au layers on PI substrate leads to formation of coarsen Au nanoislands with narrower size distribution, but the layer remains continuous. The UV Vis absorption spectra show a rise of surface plasmon resonance peak after annealing, which documents the formation of uniform nanostructure. The peak is most evident at the thinnest Au layers. The results suggest the PI is an interesting substrate capable of supporting very thin metal films and preventing their dewetting during annealing. (C) 2016 Elsevier B.V. All rights reserved.