I was cleaning my Phantom 3 Standard lens and discovered some micro scratches (I think I caused them because I didn't notice them before). I was wondering if this will affect pictures in any significant way. How do you guys clean your camera lens? Is there a proper method. I use compressed air to blow away dust, moisten up the lens with my breath, and then use a glasses cleaning cloth. I thought glass was supposed to be a bit more resilient. Is there some kind of coating over the lens? Can I somehow fix these scratches?

Scratches like that normally do not come out. You can potentially see some markings in your footage. The best course of action would be to contact your DJI Support team for a  repair service.

As a rule scratches on the front glass of a lens,  if they're small, usually aren't seen in in the image because they are out of focus. It's the one's on the rear glass that cause problems.