How do I go about filing abandonment papers against my daughters father who has had no contact with her for over 3 years, so that when my new boyfriend and I get married he can legally adopt her?

First you need to get married. Then you will have to be married a year before the courts will even consider an adoption.
Once you have been married a year, you will need to hire an attorney (you will legally need one for the adoption anyways). The attorney will be able to tell you your options.

Does the father pay child support?

If your answer is yes, then trying to terminate his rights based on abandonment is not going to work. In the courts eyes, a father who pays child support has not "abandoned" the child.
Now, if your answer is no, then yes, filing to terminate his rights based on abandonment may work. You will need to talk to an attorney and see what the legal time of no contact/support is in your area.

The easiest way to go about it all is to have the father willingly relinquish his rights to allow for the adoption. If he doesn't you have slim to none chance of convincing a court to allow an adoption by terminating his rights. Even if it has been 3 years since he has seen the child, he could decide that day he doesn't want his rights terminated and he wants to see the child, that is going to be next to impossible to fight.

There is no such thing as "abandonment papers". What you need to do is get married first, then your husband can petition to adopt the child. As part of that petition, you will need to get the father to relinquish his rights or ask the court to terminate them if you can't find him.

You should get an attorney to prepare the adoption petititon and he will take care of the termination of parental rights.