You could save it to a system file if you want, they can't be opened outside of DOS. Its not perfect but it would be a deterent, you could also encode it to the logged in user so no other user on the computer can use it (check WinAPI for this one) and you could even layer encryption on top of all that.
Mostly though thats all overkill, its best to just save it in a propriatary binary format which will deter most script kiddies, but one way or another if someone wants to edit it they will find a way.