Studying size effects on the modification of thin film physical properties requires the preparation of films with desired microstructures and stress states. For the model system of epitaxial niobium thin films on sapphire [(1120), miscut< 0.1 degrees] substrates surface topographies and stress states were systematically studied depending on the films' thickness (5 nm - 100 nm) and the deposition temperature (470 degrees C to 870 degrees C). Initial stresses, domain structures and textures of the films were characterized using X-ray diffraction techniques. The films' surface topographies were measured by scanning tunneling microscopy and atomic force microscopy, and classified into three different regimes: smooth (2D), rough (3D) and pitted (or 'meander-like'). Determination of the regimes' transition temperatures enables the tuning of the films microstructures and related stress states for each film thickness.