Like most bosses, use your surroundings to your advantage. With Dr.Ned-trap, it's best to use a Revolver or SMG (depending on skill level) and continually circle around him while shooting at his head. It's pointless to hide behind anything since he's too fast to pick off before he gets to you. Additionally, claptraps will spawn and attack as well. Thankfully, the map is open wide so you can move around freely. There are 2 areas you fight Dr. Ned. The trophy will unlock the second time you fight him (on the way to fighting the final boss going through the wayward pass). Below is a good video utilizing this strategy. Credit goes to longshotsvids.
Happy Hunting :)