When I first set up my tank it was the same, kept the filter running for a week and all the bubbles were gone. Did you wash your tank with any kind of chemicals?
Some amount of bubbles on the surface of a fish tank are normal, especially in tanks that have air-driven filters, decorative air stones, or have a hanging power filter and a low water line. If the bubbles are popping regularly and are not covering the entire surface of the tank for long periods, you should not have any long-term problems from this.
www.firsttankguide.net/aquarium_bubbles.php