Many well-known approaches exist in the literature for tolerance analysis. All the methods proposed in the literature consider the dimensional and the geometric tolerances applied to some critical points (contact points among profiles belonging to couples of parts) on the surface of the assembly components. These points are generally considered uncorrelated since the nominal surface is considered. Therefore, the methods proposed in the literature do not consider the actual surface due to a manufacturing process. Every manufacturing process leaves on the surface a signature, i.e., a systematic pattern that characterizes all the features machined with that process. The aim of the present work is to investigate the effects of considering the manufacturing signature in solving a tolerance stack-up function. A case study involving three parts has been defined and solved by means of a method of the literature, the variational method, with and without considering the correlation among the points of the same surface due to the manufacturing signature. This work represents a first step toward the integration of the design and the manufacturing in a concurrent engineering approach.