Prune all the lateral branches off the plant. Cut the branches close to the stem with sharp pruning shears. This produces a plant with longer, wider leaves. However, the plant will not produce as much cotton.
Thin the plant by removing the longer branches close to the stem. Cut the branches so the plant is balanced on all sides. This method has shown to produce more cotton in a 2006 study -- "The Effect of Branching on Cotton Plant Growth and Development," written by Dong Li, Yan Guo and Zhigang Zhan -- but the method is not widely practiced.
Cut branches off the cotton plant that are diseased or not thriving. This is rarely necessary, but it can help the plant use its energy to grow instead of trying to heal dying branches.