If you have selected files in Copywhiz using File Explorer (Windows Explorer), then go to the destination folder. Right-click inside the folder, choose Copywhiz → Paste Advanced to open the Copywhiz window and click on the 'Advanced Settings' button as shown in the picture below.
If you have Copywhiz's main window already open, then you can directly click on the 'Advanced Settings' button as shown in the picture below.
Now check the option 'Skip empty folders (Recommended)' from the source Tab, to remove all empty folders left after copying all the files.
Press the OK button and click on the 'Paste Now' button to finally copy the files and remove all empty folders that were created during this process. A sound plays indicating the successful completion of a file copy task.