Hi,
Yes you can change the shape of the rods. For this, simply double-click on your crystal to bring up the crystal lattice properties dialog and go to “Atom Waveguides in Unit Cell” area. You can pick a shape from the drop-down menu and click “add”. Don’t forget to remove the old one (delete button).
To realize a capping, you will have to modify the 3D profile of the waveguide. This can be done in the profiles and materials editor. See the documentation for more details.