Hi Eddie,
I agree with Drewhound that magnolias don't heal well. The best time to prune is after it blooms. Here's a site on how to prune.
http://www.hort.purdue.edu/ext/HO-4.pdf
Newt
don't! they will not take kindly to it. remove diseased wood and at a pinch any branch that is growing in the wrong place but a magnolia is something to leave to do it's own thing