Paper and continuous web scanners operate at varying and high temperature conditions that cause distortion of the support beams and ultimately misalignment of the scanner heads. Circulating a heat transfer fluid between the support beams and through segmented fluid channels within the beam allows tuning of the beam's deflection when operating in an uneven thermal environment. The heat transfer rate can be modulated through various techniques, including: (1) varying the flow rate through each channel under manual or automatic control, (2) controlling the inlet fluid temperature of each channel with fluid immersion heaters or coolers, and (3) setting up the flow sequence via distribution channels that are, for example, in parallel, serial, or mixed.