Check to see that you're working in the correct layer.
Alternatively, use the selection tool and right click on the fretboard. This should bring up the context menu, where you can select delete.
If you see no handles, and right clicking on the fretboard has no effect, post a link to the file here (you will need to upload the file to a filesharing service such as dropbox) or alternatively head over to the old forum (http://forum.makemusic.com/default.aspx) and create a new topic there. You'll be able to upload the file there.