Cleanliness is next to Godliness

One of the most important things to remember and I cannot stress enough to you is to clean the area in which you are making your baby food. This is super important because we are unable to achieve the amount of sterilization that factories can get. This is not a reason not to make your baby food though. All you truly must do is....
WASH YOUR HANDS!
Wash the countertops down
Clean the knives and pots in which you will be using
Clean the blender, food processor, etc.. what you are using
Make sure the ice cube trays, if you use them, are clean.
Clean the vegetables/fruit in which you are using
If you are making fruits/vegetables and meats, make sure that you change the cutting board because uncooked meat juices can transfer bacteria to fruits and vegetables.

All I am stressing to you is that you need to clean the area in which you are making the baby food.