The stain needs to be removed completely before the wood will accept a new color.

What color stain will you be using?

Sometimes it is difficult to remove stain from small lips of wood that are butted right up against the glass but yes, sanding will work. I would not use tape though because with stain, it is so loose bodied it just leaks right under the tape and will dry there. It's best to stain and then just wipe the stain off the glass with a clean rag.