A basic understanding of countermeasures requires a solid grasp on basic concepts such as Measuring the Unmeasurable and The Art of Misdirection.
Start with the fundamentals: Countermeasure 101a: The Basics and Countermeasure 101b: The Advanced Stuff (You'll Probably Never Need to Know).
Now that you've got the basics down, it's time to see countermeasures in action. Check out Examples of Countermeasures in the Real World and Advanced Countermeasures: Because You Clearly Need to Know Better (But Probably Won't).