Removing Bald Cypress Knees will stress the tree with mechanical damage to the tree. Knees occur in moist conditions. If you are not near a body of water, monitor your irrigation and watering practices. If you are on a body of water, Cypress Knees are in your past, present and future. Cutting them creates an open wound and could be an opening for infections or pests. Our recommendation is to not cut your Cypress Knees.