In order to facilitate parts assembly in a product structure, different clearances are provided in mating parts. The aim of this research is to investigate role of certain clearances in an assembly structure. These clearances are not part of tolerance stack but still can impart significant impact on product functional performance. Their influence on the product functional parameters like different stresses and deformation is studied in this research. A structure from automotive spot welding equipment is considered for this study. The effect of these clearances is determined using finite element analysis (FEA) simulations for process model of the product. It is found that some clearances are more critical for certain parameters. The results show that the product design can be improved by taking such clearances into consideration during design phase.