Smoke-wire flow visualization is used to study the development of pre-set counter-rotating streamwise vortices in boundary layer flow over a wavy surface in a rectangular channel. The formation of the vortices is indicated by the vortical structures on the cross-sectional plane normal to the wavy surface. To obtain uniform spanwise vortex wavelength which will result in uniform vortex size, two types of spanwise disturbances were used: a series of perturbation wires placed prior and normal to the leading edge of the wavy surface, and a jagged pattern in the form of uniform triangles cut at the leading edge. These perturbation wires and jagged pattern induce low-velocity streaks that result in the formation of counterrotating streamwise vortices that evolve downstream to form the mushroom-like structures on the crosssectional plane of the flow. The evolution of the most amplified disturbances can be attributed to the formation of these mushroom-like structures. It is also shown that the size of the mushroom-like structures depends on the channel entrance geometry, Reynolds number, and the channel gap.