Methods are disclosed for controlling the displacement of bearings in a wire saw machine. The systems and methods described herein are generally operable to alter the nanotopology of wafers sliced from an ingot by controlling the shape of the wafers. The shape of the wafers is altered by controlling displacement of bearings in the wire saw by changing the temperature and/or flow rate of a temperature-controlling fluid circulated in fluid communication with bearings supporting wire guides of the saw. Different feedback systems can be used to determine the temperature of the fluid necessary to generate wafers having the desired shape and/or nanotopology.