Q: I consider myself a careful woodworker, paying attention to detail. Yet, many of my flat glue-ups for which I use biscuits don’t line up on the “top,” or finished side — the side the public sees. I’ve taken into consideration the following factors already: I know it is imperative that I place the biscuit jointer on the same side of each board. I do that, and I index the boards with witness marks.
I know that the tool must be held flat and square, and I know that the tool must not move around, lest the biscuit sit in a wallowed-out hole.
I thought one of the biggest selling points of the plate jointer was to keep the tops of the boards aligned to minimize sanding after glue-up, but I’m not having those results.
A: Without knowing the misalignment you are talking about, I have to make an assumption or two. I’m guessing that you are talking about that exceptionally annoying slight misalignment that takes a frustratingly significant amount of sanding to “erase.” (Trust me, I’ve been there many times.)
Perhaps if I owned a Lamello, which is in the stratosphere of biscuit joiner quality, I might sing a sweeter song — but it’s been my experience that biscuit joiners are just not precise enough to provide perfect edge alignment.
Biscuits do help align long butt joint glue-ups. It is much easier to align and edge glue two 60" pieces together with biscuits than without them, but there will still likely be places where the edges will not meet perfectly. And I have to say that, on shorter butt joint glue-ups, say 30" or shorter, I don’t find biscuits to be of any help or benefit whatsoever. They are great for face frames, installing shelves, end grain to end grain glue-ups, solid wood to plywood glue joints — but butt joints in solid wood are not in any practical sense stronger for the use of biscuits, so why use them?
To treat your original problem, my friend Ian Kirby would tell you to get a good #07 bench plane along with a few extra irons for it — and just plane the surface flat. It will take only a few moments, and you won’t even need to sand it when you are done.