FILED FOR i539 to extend my stay for another 3 months. While application in process - can I travel outside US and come back?

When you leave the U.S., the I-539 will be abandoned. If you seek to reenter, it will be based on your unexpired visa. The immigration officer will decide if you should be admitted to the U.S. again. If you spent a long time in the U.S. followed by a short time outside the U.S., you may be refused entry because the officer may believe that you are unlawfully working or permanently residing in the U.S. Also, if you filed the I-539 before your I-94 expired, but then left after the I-94 expired but before the I-539 is approved, you should bring the I-539 receipt notice with you to show as evidence (if necessary) that you did not unlawfully overstay your I-94.