You may be confusing AF-S mode with single point mode. AF-S is selected by pressing the button in the center of the AF/M switch and holding it while spinning the rear command dial with your thumb until AF-S appears. The camera will then focus and lock for a single picture, as opposed to continuous focus for moving objects.
I think what you are after is selecting a single AF point rather than having the camera guess what should be in focus from among the 39 points. To do this, push and hold the AF button and spin the front command dial with your index finger. On the top LCD display you will see a large array of points, then a smaller array, then a single point. Hope this helps!