Use a file to take off the marked section of the bridge. I usually take it off the TOP of the bridge, so that the bottom remains flat. You you take off the bottom, and make it NOT flat, you're tone will suck and the pickup won't sound right.
Do this a LITTLE bit at a time. If you take off TOO much, you'll get string buzz, and it's time to make a new bridge.
Also, make sure your neck relief is set FIRST. Your action may FEEL too high because your truss rod is too loose.