Cameras and lenses are both precision instruments, and today's AF systems are the best we've ever seen. But there are limits to the production tolerances achievable by today's manufacturing technology, and today's high-megapixel-count DSLRs are running up against them. When you blow up high-megapixel images 100% on-screen and examine them at the pixel level, you could well see some unsharpness, even with the best gear on the best tripod and shot with the greatest care.
This doesn't mean the next new lens you buy won't work well with your DSLR, or that your new DSLR body won't work well with your current lenses. But it does mean that there's that possibility. Let's say that today's production capabilities can produce cameras within +/-5 "units" of tolerance, as well as lenses within +/- 5 "units." You may get a body that happens to be 0 and a lens that's 0, and things are great. You may get a body that's -4 and a lens that's +4, and their offsets cancel each other out, and things are still great. But you also could get a camera body that's -5 and a lens that's -5; that definitely will show in your photos.
Not too long ago, if you bought a new lens and found it wasn't sharp on your camera, you'd have to return it and try another—and maybe another, and yet another—before you found one that worked well on your camera body. Today, however, many DSLRs let you adjust for tolerance offsets via AF fine-tuning.
The theory is simple: You shoot an image of a test target using single-shot AF, then check the resulting image to see if it's sharp. If it isn't, you shoot another image with some + fine-tuning compensation, and still another with some – compensation, then examine those. One of them should be sharper than the unsharp original (uncompensated) image. Shoot another image with additional compensation in that direction (+ if the + image was sharpest, – if the – image was sharpest), and examine it. In this way, you can zero in on the exact setting that produces the sharpest focus.
You can do this using a newspaper or magazine page taped to a wall, but a target designed specifically for the job produces better results more easily. One such device is LensAlign (mtapesdesign.com). This consists of a vertical focusing target and a finely calibrated angled ruler that's easy to set up and align precisely, and that shows just where your AF system is focusing—on target, in front of target or beyond target. You can examine your test images on your computer monitor and quickly determine whether your camera/lens combo needs AF fine-tuning, and if so, in which direction. You then can adjust the AF fine-tuning accordingly, shoot another test image, and check that. If your camera has live-view capability, you don't even need to shoot test images: Just magnify the live LensAlign target image 100% on the camera's LCD monitor, and examine it.
Most cameras with AF fine-tuning let you save specific settings for a number of lenses and then apply that correction automatically each time you mount that lens. Note that zoom lenses may require different corrections at different focal lengths, so test at the focal length you use most often.
1 Mount the camera on a tripod so you don't inadvertently move it closer to or farther from the test subject as you take test shots, and so camera shake doesn't affect the results.