Rust Stain On Quartz Countertop . Apply the paste to the stain and then cover it with plastic wrap for trickier stains. Allow 10 to 15 minutes for the saturated. Pin on **Put A Pin On It** from www.pinterest.com Then let the soaked cloth sit on the stain for 10 minutes. One of the best ways to remove rust stains from granite countertops is with a physical abrasive. Put a cast iron dutch oven on the counter for about an hour and when i moved the cast iron there was a perfect rust stain circle.