I saw a very old question (unanswered) about this. I have made a Yiddish font and want only the boxes I've edited to appear in my font (makes it easier to edit the font). I know different typefaces present with more or fewer of these glyph boxes so it must be possible somehow. Can Type Tool 3 remove the boxes?

You could create a custom "encoding" file (.enc) that references only the glyphs you want to have in the font.