For a DSLR, accurate AF relies on both the mechanism and the firmware adjustment. The AF adjustment parameters for the firmware are stored in the camera's flash memory and can not be accessed directly.
When the factory setting of the AF adjustment values is no longer suitable, the AF system will become inaccurate. Part of the AF points appear front or rear focus is a typically symptom. This might because of the body's mechanism is aging or the AF adjustment parameters are simply not well adjusted.
Options we have for this issue are:
a, go to the Nikon service site and pay for an adjustment.
b, use the Service software and DO IT YOURSELF
The following link contains the detailed guide on the option b (without the loss of the generality, D90 is used).
http://t.cn/8sBonLa
The setup: (The laptop runs the service software. The camera is mounted horizontal. The test screen on the left is required to be placed as far as possible and perpendicular to the view direction of the camera.)

Prepare the file and put into the software's directory:

Prepare images for the software:


Follow the steps:



And skip the two:


Now the adjustment begins:

When this appears, put the image with horizontal lines on the test screen.

When this appears, put the image with vertical lines on the test screen.

The new adjustment values will be written into the camera by the software:

After the above procedures, the software will runs an additional AF inspection with identical process.