Two different roughening mechanisms are studied using a production-ready epitaxial deposition system to grow various epilayers, including the base layer of bipolar transistors. Surface roughness is measured using atomic force microscopy and transmission electron microscopy is used for cross-sectional analysis. Very smooth surfaces are routinely obtained, with a root mean square roughness of 0.15 nm. However, two possible mechanisms are shown to increase surface roughness under certain conditions. Above a certain critical thickness, for growth temperatures higher than 525 degrees C and Ge compositions above 25%, strain redistribution results in surface ripples with a typical wavelength of the order of 100 nm. In addition, we find that substrate contamination (C,O) can produce wide depressions, several hundreds of nm wide and on average 10 nm deep in Si epilayers. The addition of a small concentration of Ge (below 15%) seems to produce more planar growth compared to the same thickness (50 nm) of Si only. The origin of the different surface morphologies observed is discussed.