In this work, atomic force microscopy (AFM) investigations of lamellar PS-b-PMMA block copolymer layers are performed during the self-assembly process. These in-situ experiments are made on both un-patterned planar substrates and topographical substrates (graphoepitaxy experiments) at different temperatures and for different durations. Image processing software is used to produce AFM movies of the same location on the sample and to measure polymer micro-phase domain lengths versus annealing time. We observed that micro-domain formation starts after only a few minutes of heating. On planar substrates, the micro-domain length evolution with time (t) is in accordance with the literature, following a power law~t0.29. On the other hand, in substrate channels and in conditions used, we show that the domain length dependence follows a two-step process. Initially, the system adopts a similar kinetic dependence as that of the planar substrate, but at longer times, drastically reduced time dependence is observed due to the topographical confinement of the domains.