Good advice from the Journal of Biblical Counseling on how to helpfully counsel unbelievers. From J. Alasdair Groves' “How Do You Counsel Non-Christians?” which is well worth reading in its entirety:

1. Don’t forget the obvious: know and love the person. Counseling involves building a friendship.
2. Help the person look in the mirror. Ask good questions that help the person see their motivations and reinterpret their life.  
3. Find out what the person thinks about God. Very often, the person rejects a version of God who has very little to do with the God of the Bible.