Clone troopers are mobs that belong to the republic/Jedi. They will attack you if you belong to the Sith or if you are a Bounty hunter. An important thing to note is that clones spawn in groups of 3-5 mobs, and are rarely alone.
For Sith, the best way of dealing with a clone is to deflect their blaster fire, frontflip over them (Jump + Sneak + Forward) and kill him before he turns around to face you.
For bounty hunters, seek cover, and pick them off either using a low power (blaster pistol, blaster XRC, blaster AVR) or a high powered blaster (Sniper, rocket launcher, tusken cycler,dc-16 laser rifle)