Well, a full exhaust would be your exhaust manifold(s) (like headers) the y pipe , then from the catalytic converter all the way to and including the muffler is also known as the Cat Back , all these things are what make up your exhaust.
So based on what you are asking the full exhaust would be the Full CAT BACK exhaust.
The muffler is just that part at the end of the piping... sonmetimes the axel back
So the rest of the piping can be stock with a after market muffler...