It would have been best to remove those branches when the tree was dormant.  Otherwise, pruning spring flowering shrubs is done after they bloom.  But cut those branches off now.  I am surprised your magnolia is not blooming.  Perhaps it is now being shaded by other trees.  If you want to fertilize, do so lightly.  Like other trees, magnolias take nutrients from the soil around it so if it is near a lawn, the lawn fertilizer is available to it.