To create a stepped beam with different cross-section areas in ANSYS 13, users must define nodes at the points where the cross-sections change. The process involves creating two distinct cross-sections and assigning them to the appropriate beam elements between the defined nodes. Users should utilize the Beam element 188, ensuring to set real constants and mesh the elements correctly. If facing issues with meshing, it is recommended to create keypoints and lines instead of relying solely on nodes. Finally, for free-free boundary conditions in modal analysis, no constraints should be applied.