The pruning of the tree links to the idea that some level of action is needed to undertake change and viability for an organism.  The pruning of the tree involves some level of severing or shedding of one's past in order to receive the present and the future.  There are parts to the tree that are "diseased" and, while it might seem cruel, it is a form of life in order to sustain life.  This ties into Melinda in a couple of ways.  Melinda has been "diseased" in her past with the rape perpetrated upon her by "IT" and the social stigma that resulted from it.  She has been tainted by the challenges of social acceptance and how these issues have been internalized into her own psyche.  The pruning that is needed for Melinda is for her to be able to shed these elements and enable her to become her own person in a new setting and in a new condition.  This becomes one of the elements where Melinda's metamorphosis, or sense of change, is paralleled to the natural way of life.  The natural world, especially with trees, connects to the life force that runs through Melinda and the element of pruning is a part of this.