Noise (from autofocus?) during Video on DSLR
The noise you talk about is usually caused by lens motors related to autofocus and motors, related to image stabilization. The best you can do is to use external microphone and connect it to microphone port of the camera. This will give you better isolation of the recorded sound from camera noises and better sound quality.

Of course you can always use external sound recorder and sync video and sound in post.

EDIT: to avoid the noise from focus motors you can use manual focus. To avoid noise from stabilization motors (if any) you can switch off image stabilization (VR, OS, IS or whatever it is named) and use rig with stabilization or tripod.