Commander Shepherd knows what they are and how to take care of them. She also has armor that we can wear that doesn't stop them hurting you but makes it easier to take.
The little one were formally alive and can be taken out the way you would anything else. Head or heart. There's something called banshees that you just need to avoid, she says they can mess with your head. The big robot ones can only be taken out from inside, but it's not as simple as just shooting them. There are pathways and failsafe to get through. And you have to avoid the red beams at all costs.