The actual cut is very important because it not only effects the appearance of trees, they also effect the trees response to the very cuts made. Growth, vigor, and wound wood formation (tissue formed after pruning or wounding) are all influenced by the location and type of cuts made. That is why the tree care industry has created a set of standards, American National Standards Institute, ANSI A300, that professional arborists use when considering pruning trees and plants.
Flush cuts through the branch bark ridge or collar (if present) cause the development of many sprouts and weak branch formation. This type of cut interrupts the food and water supply by severing the phloem and xylem, critical pathways for food and water, leading to dehydration and death of the tissue.
Natural target pruning is the correct procedure and the industry standard used by informed arborists. It means cutting close to the branch bark ridge without cutting into the ridge or collar. It is also very important that branch stubs never be left, because it can lead to the formation of cankers in many trees and prevents closing of the wound, leaving the area open to decay. The angle of the cut is also very important, and should be made in the opposite direction to the branch bark ridge creating an imaginary triangle. This type of cut is only done on trees with no collar present.
There are many reasons to prune a tree, health and safety are the first and most important which brings us back to the importance of correct pruning.