From what I understand, and I have seen, normally what CSE does in regards to paternity is summon the alleged father to court. He has his chance there to deny paternity or not. If he denies paternity, then they will order a paternity test. They will also accept an Affadavit of Parentage. If he doesn't show up, then he is presumed the father and you'll win by default.
III. ESTABLISHING FATHERHOOD: PATERNITY
A father can acknowledge paternity by signing a written admission or voluntary acknowledgement of paternity. All States have programs under which birthing hospitals give unmarried parents of a newborn the opportunity to acknowledge the father's paternity of the child. States must also help parents acknowledge paternity up until the child's eighteenth birthday through vital records offices or other entities designated by the State. Parents are not required to apply for child support enforcement services when acknowledging paternity.
Under the Personal Responsibility and Work Opportunity Act of 1996 (PRWORA) an acknowledgment of paternity becomes a finding of paternity unless the man who signed the acknowledgment denies that he is the father within 60 days. If it becomes necessary to seek child support, a finding of paternity creates the basis for a child support order. A support order against the father cannot be established for a child who is born to unmarried parents until paternity has been established.
It is important to establish paternity as early as possible. While CSE offices must try to establish paternity for any child up to the child's 18th birthday, it is best to do it as soon after the child's birth as possible. If the man will not acknowledge that he is the father, the CSE agency can order genetic testing. These tests are simple to take and highly accurate.
What if he denies he is the father, or says he's not sure?
Paternity can be determined by administrative procedures which take into account highly accurate tests conducted on blood or tissue samples of the man, mother and child. Genetic test results indicate a probability of paternity and can establish a legal presumption of paternity. These tests have an accuracy range of between 90 and 99 percent. They can exclude a man who is not the biological father and can also show the likelihood of paternity if he is not excluded. Each party in a contested paternity case must submit to genetic tests at the request of either party or the CSE agency.
The father of my child said I would never get a paternity judgment on him because he'd just leave the State. What happens in this case?
If the accused father fails to respond to a formal complaint properly served upon him, a default judgment can be entered in court. The default judgment establishes paternity. At the same time, a court order for support may be issued. If the parent has disappeared, State and Federal Parent Locator Services can be called on to help find him. States must give full faith and credit to paternity determinations made by other states in accordance with their laws and regulations.
http://www.acf.dhhs.gov/programs/cse/fct/cshdbk.htm