Sorry, but you can't just "file paperwork" somewhere and make it happen.
A name change not associated with an active divorce case or associated with a marriage would need to be handled through a suit for change of name, which is an actual lawsuit (although not adverse, obviously) under the Family Code, and yes, she would have to file an application, get fingerprints, and then appear and testify in front of the assigned judge regarding the reasons she wants the name change. Based on what you posted, there shouldn't be any problems (not doing it for an illegal reason, like trying to avoid creditors, etc.). The filing fees are about $300 just to the court. I would suggest your wife hire an attorney to assist with this matter - even though it's non-contested, there are rules of court procedure that most laymen are not familiar with.