Aperture wide open … Small depth of field is ok.

Be mindful of vignetting around the edges of your lens. Unless you have very expensive glass, it’s likely you can’t get both the center and the edges of your frame in focus at the same time when shooting at a flat surface a short distance away from the lens thanks to our good old friend spherical aberration, and it’s even less likely if you have it wide open. There’s probably no harm in stopping down slightly and taking a longer exposure to compensate for this as much as you can, because your photos aren’t going to move. You might want to take a couple of test shots against a grid background or something to determine just how large the sweet spot of your particular lens is at that distance.

You can avoid this by backing the camera up from the subject some more, too, but I figure if you’re trying to preserve photos by taking further photos of them, you probably want to get as many of your sensor’s pixels across them as possible.

Use a tripod (any old).

I don’t know about yours, but none of my tripods are capable of pointing straight down and truly getting the camera perpendicular to the surface they’re standing on without the center barrel of the tripod itself being right spang in the middle of the frame just below the horizontal centerline. And that’s even if the head on your tripod can tilt down a full 90 degrees at all, and without some part of your camera or lens bonking into it. Even extending the idiot stick won’t help you any, because the mount and pivot head is out at the end of it rather than before the point where it extends from. (Maybe some kind of high dollar, high speed David Attenborough top flight pro rig tripod has a second pivot placed before the extension tube, but I’ve certainly never owned one set up that way.) When I have to do a true top-down shot for one of my myriad reviews, I always wind up hand holding the camera for that very reason.

Other gimcrack ideas involving 2x4s and spirit levels and 1/4-20 screws or mirrors suggest themselves, but the realistic outcome with a normal tripod is that you’ll wind up with your camera not quite square to the table and thus all of your photos-of-photos will wind up keystoned to some degree and this will drive you nuts. Perhaps you’d have better luck and spend less money just propping up one end of the surface you’re putting your subject photos on to get it perpendicular to the lens without getting any of the tripod itself in the shot.

Users with access to a remote shutter release can dispense with the self timer trick (but hey, I don’t knock it — I used to use the 2 second self timer on my camera as a vibration settling delay all the time when I was young and broke) and make their workflow speedier and significantly less annoying.