The three dimensional swirling flow has been obtained by solving Navier Stokes equations, expressed in cylindrical coordinate system, using finite difference technique on a staggered grid. An explicit finite difference method using pressure correction technique, for the solution of Navier Stokes has been implemented to solve three dimensional flows. Present study explores the 3-D axisymmetric nature of stratified swirling flow and vortex breakdown in a cylindrical annulus cavity with top rotating lid. The annulus is obtained by inserting a thin coaxial rod in cylindrical cavity. This rod may be stationary or rotating depending on the particular study. Three dimensional swirling flows in annuli have also been studied subjected to axial temperature gradient or under the influence of axial magnetic field. Influence of governing parameters Re, Ri and Ha on the overall heat transfer has been investigated through variation of the average Nusselt number with these parameters. Further, the present numerical results are shown to be in good agreement with the available benchmark solutions under the limiting conditions.