Applications of morphological filters for two-process profiles were analysed. Dilation, closing and alternating sequential (closing + opening) filters were used with a circle (disk) as a structuring element. An original method of a disk radius selection was elaborated for two-process profiles. This procedure was applied for many simulated and measured profiles. Behaviors of morphological filters were compared with those of double Gaussian (Rk) filter. Robust filter was also taken into consideration. In calculation, TalyMap software was used. The proposed procedure was found to be very useful. It was developed for 2D profiles but it can be easily extended for an areal (3D) surface topography filtering. From among morphological filters, the alternate sequential filter is suggested.