Gently peel off the nearest corner to the bubble with a piece of scotch tape. With your other hand, dab a second piece of scotch tape underneath the film (depending on what's causing the bubble, either toward the film or away). When you let the film re-apply itself to the glass, use your finger to help smooth the film against the glass in a downward stroke toward the top or bottom edge.
Yea, I had some bubbles on the sides that wouldn't go away either. Eventually got em though.