You are correct. ideally you should do this with a notched straight edge - as you can assume the fingerboard was once flat, even if the frets aren't, You can buy them fairly cheaply, or a bit of straight solid aluminium strip and a file will see you with your own home made one in 30-60 minutes. Just mark off the fret positions on the strip, then file a suitable sized notch in each position so that it will sit over the fret without touching it. Always useful in setting up your own guitars. You can do exactly the same thing for a bass (though you obviously need a longer metal strip ).