The present study investigates the planar Couette flow problem for low Reynolds numbers inside a rectangular duct with a morphing cavity serving as a vortex formation promoter. A finite element code implemented in COMSOL Multiphysics is employed to analyze the effects of the cavity aspect ratio and variations of the Reynolds number on formation and topology of the vortices within the embedded cavity. The obtained results indicate that the cavity height is influential in the number of vortices. It is shown by increasing the Reynolds number, a single vortex tends to move towards the outlet. In addition, streamlines demonstrate that small vortices in vicinity of the cavity corner tend to be enlarged with increase of the Reynolds number. The developed numerical model can be extended to the flow structure of natural systems such as an embayment subjected to parallel-to-shore currents.