Ideally, you would have removed or cut back these whippy branches in August. I'm assuming your tree produces its fruit on spurs......if espalier they would be.......and you prune in late summer to encourage fruit. I would cut back those whippy,shoots......they won't produce fruit.....now probably to just a few inches from the base. The idea is to produce short stocky shoots....spurs....along the branches and this is done by summer pruning.