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The D90 has three different autofocus modes. In the AF-S mode it will not shoot until it has focused. In the AF-C mode it will shoot when you press the shutter release button even if has not focused. In the AF-A mode the camera switches between the AF-S and AF-C modes so either can apply.Also, bear in mind that the camera doesn't really know what you're taking a picture of. It may focus on something other than your subject. If you're in the single-area AF mode then you control which of the eleven focus points the camera uses. In any of the dynamic-area AF modes the camera decides.For full details on how the various modes work, please consult your manual. You might also check out the Nikon D90 video tutorial.
1. Use the slider switch on the left of the camera to set it to MF (manual focus). The focus ring is an electronic one rather than a physical control like the zoom ring, so the response can seem slow.
2 Go into the camera menu and enable DMF (Direct Manual Focus). This allows you to override the autofocus simply by adjusting the focus control, but it does not work if the slider switch is set to the AF C setting (continuous autofocus), it only work in the AF-S (AF only activates once when the shutter is half pressed).
Try checking C.Fn III, 3: AF point selection method. Yours might still be on option 2.
0: Normal - Works by pressing the AF Point button and then the Multi-controller.
1: Multi-controller direct - Press the multi-controller to directly select an AF point (without first having to press the AF Point button). Pressing the AF button reinstates all AF points for auto AF point selection.
2: Quick Control Dial direct - turn the Quick Control Dial to select AF points. In this mode, AF points will not be displayed on the LCD panel.
Sounds like you need to get your camera fixed by Nikon.
However, you say the auto focus stopped working, you didn't switch to a lens that uses a mechanical focus linkage do you? The D40 only supports lenses with AF-S or AF-I type autofocus drives. AF-D and AF-G types without AF-S or AF-I don't autofocus.
Also, check that the A/M switch on the lens is in the correct position.
Manual focusing is quite difficult to do accurately with an AF camera. The screen inside the camera is not optimized for this. If you are sure you are focusing accurately but the pictures you take are still out of focus, the mirror may need adjusting. I can provide further info on this if you require, but if you're within warranty, i'd recommend that route first.
There are four focus modes: S-AF (Single auto focus), C-AF (Continuous auto focus), MF (Manual Focus), and S-AF/MF (Simultaneous mode).
(SINGLE Auto Focus): Focusing is performed once when the shutter button is pressed halfway.
C-AF (CONTINUOUS Auto Focus): The camera repeats focusing while the shutter button is pressed halfway.
(MANUAL FOCUS): The function allows you to manually focus on any subject while looking through the viewfinder.
SIMULTANEOUS USE of S-AF mode and MF mode: You can fine-adjust focus manually by turning the focus ring after AF is performed in the S-AF mode.