This study investigates the dynamic behaviour of machine tool structures, focusing on the impact of structural changes on natural frequencies and machining performance. Variations in machine tool dynamics, such as natural frequency shifts, significantly affect tool stability and machining quality, particularly in high-performance cutting. Numerical model predicting natural frequency changes due to structural modifications was developed and validated experimentally. The model indicates that structural changes lead to variations in the different position values, which influence the natural frequency of the tool. In parallel, this research explores the structural integrity of 5-axis CNC machining centers, vital for advanced manufacturing. FEA program is used to establish natural frequencies and mode shapes, while experimental modal analysis (EMA) validated these results, with discrepancies of around 10%. A detailed spatial analysis revealed significant variations in deformation and natural frequency across different spindle positions, influencing rigidity and machining accuracy, especially for larger work pieces. The findings provide insights for optimizing machine tool design, enhancing performance, and paving the way for future research in improving structural integrity for advanced manufacturing systems.