Advancements in machining technology demand higher speeds and precision, necessitating improved control systems in equipment like CNC machine tools. Due to lead errors, structural vibrations, and thermal deformation, commercial CNC controllers commonly use rotary encoders in the motor side to close the position loop, aiming to prevent insufficient stability and premature wear and damage of components. This paper introduces a multivariable iterative learning control (MILC) method tailored for flexible feed drive systems, focusing on enhancing dynamic positioning accuracy. The MILC employs error data from both the motor and table sides, enhancing precision by injecting compensation commands into both the reference trajectory and control command through a norm-optimization process. This method effectively mitigates conflicts between feedback control (FBC) and traditional iterative learning control (ILC) in flexible structures, achieving smaller tracking errors in the table side. The performance and efficacy of the MILC system are experimentally validated on an industrial biaxial CNC machine tool, demonstrating its potential for precision control in modern machining equipment.