Results of experimental study of influence of spanwise flow nonuniformity on the wave train evolution in supersonic boundary layer at Mach number M = 2 are presented. Spanwise modulation of mean flow in a boundary layer was created by means of labels from scotch tape by thickness of 60 and 110 microns. Downstream evolution of controlled disturbances was investigated. The wave characteristics of traveling disturbances were obtained. It was found that the wave trains development depends from size and location of the roughness. It is shown that the wave packet evolution qualitatively has the similar development in both cases as for the smooth surfaces. At the same time, the spanwise modulation of the mean flow leads to the fundamental wave excitation with high inclination angle. The phase spectra indicate that excitation of these waves takes place in the center of the wave packet. It was shown, that mean flow modulation can lead to stabilization of disturbance development in supersonic boundary layer on a flat plate.