This numerical study deals with the dramatic change of the votex shedding process by controlling a shear layer separated from a circular cylinder at low Reynolds number. The control of the flow is established by introducing a fine circular cylinder(the control cylinder) in the neighbourhood of the main cylinder. Controlled vortex shedding process in the multiply connected domain which is reduced to the viscous region near the bodies and their wakes was analyzed by the FEM-FDM blending technique. The vorticity-streamfunction formulation is used to solve the incompressible Navier-Stokes equations with the time dependent wall streamfunctions determined by the pressure constraint condition and far field streamfunctions from the integro-differential formulation by the Green's theorem. The standard Galerkin finite element method is used to make grid system convinient to apply in the relatively small and multiply connected subdomain, and the finite difference method based on the general coordinate system is employed in the rest of the computational domain. An impulsively started single circular cylinder flows are solved by the present method in order to test the efficiency and reliability of the method and the results are compared with the earlier experimental and computational results. The numerically analyzed data for the controlled vortex shedding process are used to examine the effect on the alteration of the vortex shedding processes, the time mean and fluctuating fluid forces, and the vortex shedding frequency due to variation of the position and diameter of the control cylinder for the Reynolds number of 100 and 200. Furthermore, such a deformation of the separated shear layers, namely, the position and region of their roll-up, are discussed in detail based on the calculated results which are the instantaneous vorticity field and streamlines.