In Windows FTM, if you put misc stuff into "Research Notes" and mark all Research Notes as Private, or mark any other note private, when exporting, you can unselect the option to:
__ Include Private Notes
You can also unselect:
__ Include Private Facts
to get rid of your copy and paste of database items you have pasted into Fact Notes, like census transcriptions and such.
Otherwise, notes will be exported and you'll have to go to the exported file to erase them.
Try it and see what happens!