You have two good choices:
1) leave it and let your fig grow into bush form with 3-5 main trunks.
2) let the sucker harden, then separate it from the main tree with a sharp spade this fall and pot it up as a new tree.
I would decide based on zone. If you are in 8 or higher, grow the fig as a tree - thus separate the sucker. If you are in zone 7 or lower, grow as bush form. They tend to do better with cold winters.