I own my home and me and my boyfriend shared the home for the past 2 years and have a 2 year old son together. We are now separated and he refuses to leave. The mortgage and all bills and utilities are in my name. How do I file to evict him?

Like any of the thousands of others on this forum who have an unwelcome houseguest: sue to evict him.

You should also sue him for custody and child support while you are at it.

By the way, your statement that "We are now separated and he refuses to leave" is contradictory:

If he refuses to leave your home, you are not yet separated.