The details of flow dynamics during the interaction of a microwave filament (regarded as heated rarefied channel) with an aerodynamic body in supersonic flow are considered. Flow control via the effect on the frontal drag force is discussed. The mechanisms of the drag force reduction for a symmetrically located filament and temporary drag force enhancement for an asymmetrically located filament are established. These mechanisms are attributable to the vortex structures forming via the instabilities in front of the body and inside the shock layer. Three kinds of flow instabilities inside the shock layer are analyzed numerically. These are the Richtmeyer–Meshkov instability, the shear layer instability of Kelvin–Helmholtz type and the instability of a flat-parallel tangential discontinuity. The last instability is shown to be accompanied by generation of steady flow structures. A comparative analysis of the resultant vortices and structures is conducted. Limited length and infinite length filaments are considered. The flowfields are investigated for freestream Mach numbers equal to 1.89 and 3, and a wide range of filament characteristics.