Not with a D3, but with a D7000. I used the AF Fine Tune menu with proper calibration tools and methods to adjust for the lens. If you can't get it calibrated using the menu then you might need to contact Nikon. Is it with every lens or just one, in a particular situation?
Look in the setup menu for "AF Fine tune". You can then calibrate each lens separately. It's well worth it when you find back or front focus issues with some lenses.
I used the Reiken Focal software to AF Fine tune my D800. I had to send it to Nikon to get the 70-200 with 2x teleconvertor sorted as it was out of range.