angel,
to use NACA for a modification it works the same way as it would through the servicer...............they are a non profit counseling agency that will put together a modification proposal based on their affordability equation which they will check when they go over your financials with you in the counseling session....and then they present the proposal to the investor for approval through the servicer...........it won't hurt you to try if you meet the criteria because the services are free........ Their criteria is that the home is owner occupied and that is is the only property you own.
click on the link for the submission instructions.
https://www.naca.com/refinance/refinanceSubmission.jsp