Indeed the 'Copy Supermesh Element' functionality is one of the very few functions that have not (at least not yet) been rebuilt in the new user interface. I would recommend to either prepare the polygons in a GIS system, using the copy functionality there, or - if you really need the functionality in FEFLOW for your specific application - to install FEFLOW 6.0 in parallel. You can create a smh file in FEFLOW 6.0 Classic and bring it into 6.1 for mesh generation.