With a view to improving the realisation of polymer optical waveguide some features relevant to the photolithography process are analysed. This paper focuses on defects that occur on the surface of polymer layers involved in the process. For example, depending on the heat treatment or the deposited material, some worm-like defects appear on the polymer surface. When they occur, the waveguide surface roughness becomes too high (about one hundred nm and more). This means that the optical performance of the waveguides is too poor. In this document, we show the changes in temperature on polymer film surfaces which are coated with a thin inorganic layer and the occurrence of these defects is observed. This work confirms that the defect occurrence is clearly linked to the glass transition temperature. The paper reports that, in some cases, the adjustment of thermal properties by annealing can advantageously shift the glass transition, without changing the target optical properties.