Joint tenancy with the rights of survivorship in new york state

I called the county clerks office to see how to get a deed in solely my name since my mother is deceased. They said to contact an attorney. When one owner dies their interest in the property automatically transfers to the survivor. So I thought that it would be relatively easy to resolve it and get a deed solely in my name. I need to see an attorney at any rate for other issues but does anyone know what the process is?