A few additional notes.
In the picture in the original post, the system is set up way too "minimalistic". The electrodes are too short in Z, as is the central region.
On the other hand, for the electrode band structure calculation you do indeed want the minimal electrode, to avoid zone folding but also to make the calculations faster.
There is a tool in VNL to extract the electrodes from the device configuration (a button on the left-hand side toolbar), but it doesn't reduce them to minimal. So the procedure I would recommend is to make a dopy of the device configuration, convert it to bulk (click the "Bulk" button), then again make a device from it, but this time with the minimal electrode (shortest possible length suggested in "Device From Bulk") and then finally extract the electrode using the "Split Device" button.
