What it should do is first, allow you to jog the position to one corner of the scanning area. When you hit enter to accept the first point, it will lower the bit to surface to allow you to verify your starting position. If you are happy with the first point, hit enter again to accept it. If you want to change the point, use the arrow key to adjust the positions.
Once you hit the enter key (the second time) to accept the first point, you will be prompted to move to the second point. So just repeat the process of the first point.
If this is not what you are seeing, can you describe in more detail what it is doing? For example what messages are you seeing on the display?
For none rectangular scans, the import software will allow you remove the background so that your pattern appears the same shape as the original piece.
Chris Morlier
CarveWright