Based on a low-cost fabrication routine microstructured conducting polymer films of poly (dioctylfluorene-co-benzothiadiazole) (F8BT) are prepared without any heat treatment or vacuum steps. The influence of thermal annealing at temperatures below the glass transition temperature of F8BT on such microstructured channel structures is investigated. In the applied structuring routine, a F8BT film is spin coated on a channel-type hard master structure and afterwards floated on a flat support. Thereby, the properties of the final polymeric structures, for example channel width and height, can be tuned by simply varying the polymer concentration in solution and using the same master structure. With in situ grazing incidence small angle X-ray scattering and imaging ellipsometry the installed channel structure and the influence of thermal treatment are probed. A complex interplay between a macroscopic polymer flow (reduced channel heights) and a molecular rearrangement (formation of mesoscopic crystallites) takes place during thermal annealing. (C) 2012 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys, 2012