You can delete a system simply by clicking on it's name in FreeSCAN, to select it. Then, if you right Click on it, you'll get a pop-up menu with various actions you can take, including deleting the system.
With the system selected in the file, you can also choose Delete from the drop-down Edit menu, or bu using the shortcut <Shift>+<Delete>.
Those actions would delete it from your file in the software. Unless you manually delete the system on the scanner itself, the system will remain in the scanner until you either manually delete it, or write the edited file to the scanner. When you write a file to the scanner, you have the options to delete all systems before loading the new file, or deleting any existing system that has the same name as one you writing to the scanner.