I am currently trying to gain sole custody of my daughter. Her father recently fled to another state due to warrants out for him. She is 3 years old, and he started taking care of her half the time when she was 1 1/2, and lasted for about 6 months or so. So, he has not been around for much, I'm just worried about if he might come back and try to take her. I don't know what steps to take first.

Are you married to him ?

But you need to file for custody and ask for him to have no visits due to his outstanding warrants.
Also if he has a long history of prison time, you may even get his rights taken away ( but not as likely)

If and when he clears up his legal problems he may get some limited visits