If i am clean my last 3 months of the pregnancy off cocaine. will the baby show positive for drugs when born and they test him?

It depends...: on where you go for delivery. Be prepared that the hospital's policies stipulate patient drug testing, and testing of the baby's stool.

No: If you are clean for the last 3 months of the pregnancy then the baby (or you) will not test positive. However, the most damaging effects of drug use to the fetus occur in the first 3 months. You need to ensure that your baby is properly evaluated for it. I commend you for being clean for the last few months. Keep it up and don't be afraid to get help.