Industrial demand for manufacturing large sized work pieces with intricate designs has been on the rise. In order to improve the machining processes, CNC machines are adopted due to their high speed and precise manufacturing capabilities. In these machines, optimization of certain parameters plays a significant in their dynamic and static characteristics. Numerous existing algorithms are used for designing an efficient CNC, with each one dedicated to optimize a specific parameter of the machine tool. This work proposes a novel design algorithm for designing a CNC machine tool gantry with columns which is mounted on a well-designed feed drive system. The objective of the current research, is to design a gantry type machine tool with high rigidity and optimal weight in order to reduce vibrations of the machine and improve the surface finish of the finished product. An algorithm is devised in the present study to achieve the optimal gantry design. Algorithm devised in the present study reduces the mass and stress level with application of stiffeners, strategic removal of weight, minimizing computational complexities, and maintaining considerable rigidity. The design is analysed by FE method for calculating rigidity, stresses and deformation according to the applied boundary conditions. The shape optimization provides the optimum shape of the gantry required for its specific design purpose. In the present research that design purpose is to fabricate a gantry integrated with columns for an 8 feet by 4 feet CNC Router. The topology optimization technique is applied on the optimal shaped gantry to achieve further weight reduction. Strategic reduction of weight enhances the stiffness and the natural frequency. The modal analysis results of new gantry assembly are compared with the natural frequencies of existing models to communicate the effectiveness of the proposed optimization methodology. The proposed design of the gantry is also tested with the help of laser vibrometer to estimate the natural frequency at which the machine can function without attaining the resonance condition.