Chance of getting into engineering PhD if I have good references and research experience but don't satisfy 3.0 GPA requirement? I graduated with 2.7 undergrad, and currently pursuing a masters degree and will graduate with 3.3. I plan to apply for PhD programs in engineering for 2017 Fall. 

Here is my question: Many schools state that they require 3.0 GPA or so, but how do I know that whether they intend undergrad GPA?

Do you think should I apply to such school that states that


  Minimum GPA: The MS and PhD program has a minimum GPA requirement of
  3.0 on a 4.0 scale. 


?

Is it waste of my time if I have stellar letters of references and cool research experiences?
My undergraduate GPA was much lower than yours. My MSc GPA was also lower than yours. I got admitted to a top 40 US school (engineering and fully funded). I had good recommendation letters and few journal publications. This was five years ago. I know there are few guys here who have similar GPA, etc as your. So, It's very possible!