If you want to eliminate a waypoint (not a whole waypoint file) right click on the specific waypoint (on the map or the data tree) and select ‘Eliminate waypoint’. If you have opened just one waypoint file, you can close it selecting ‘Waypoints > Close waypoints’.
If you have opened more than one waypoint file, select ‘Waypoints > Close waypoints’ and you will close the first file you opened. If you have opened more than one waypoint file and you want to choose a file to close it, you will have to go to the data tree. Right click on the name of the waypoint file you want to close and select close waypoints.
If you want to close all the open waypoint files and all the open elements, select ‘File > Close all’ in the main menu.