If it's in the trunk--no, sorry, RIP for your little tree. Even if you cut it low enough on the trunk, the chance of reinfection is so great you wouldn't want to waste any more time on it.
The good news is it's early spring, so you have time this year to start over ASAP.
You might want to choose a new variety and a new spot, in case it's in the soil.

Carla in Sac

I knew that I would need to cut it down... Until I cut it down is there a way to protect my other fruit trees from the Canker- I have two apple trees and I am planning on getting a peach tree.

Apple trees are not in as much danger as stone fruits. Apricots and cherries are most at risk, then plums, then peaches and nectarines. I would avoid planting in the same hole in case the disease remains. UC Davis says there is no spray that really works (including copper), that the best practice is to choose varieties and rootstocks which are resistant when canker is a problem for you. They say Lovell is the most resistant rootstock, and this chart says the same. (page down for the chart)

http://www.fowlernurseries.com/New%20Pages/Rootstocks.htm

Carla in Sac