Finite Element Method (FEM) analyses have improved the process of designing modern machines, especially when the effective construction solution has to be found. In the paper authors have presented the application of these analyses based on the example of the construction of the punching die for belt perforation. For these machines the cooperation of the piercing punch and the die is crucial. Because of this, the analysis of the flexural rigidity of the head block and the punch plate provides useful information, which can be used to maintain proper alignment between the punch and the die during the perforation process. It may have positive effect on the tool wear and the performance of the punching. Additionally, by using the topology optimization the mass of the punching die can be greatly reduced while maintaining enough rigidity. This effect is desired in automated machines for belt perforation, in which the punching die has to move with high velocities in order to create a designed pattern on the perforated belt with satisfying efficiency. In the presented research authors focused on determining the influence of the constructional parameters of the punching die on the deflection of the head-punch block. Obtained results and the presented methodology of performing the FEM analyses of such machines will help to improve their design process and find the effective construction solution.