In the design step, the realistic modeling of the product represents an industrial requirement and a digital muck up (DMU) improvement. Thus, the tolerance integration in the computer aided design (CAD) model with the neglect of important physical factors, such as the components’ deformations during the mounting and assembly operation, causes a deviation between the numerical and the realistic models. In this regard, this paper presents a new model for the tolerance analysis of CAD assemblies based on the consideration of both manufacturing defects and deformations. The dimensional and geometrical tolerances are considered by the determination of assemblies’ configurations with defects based on the worst case tolerancing. The finite elements (FEs) simulation is realized with realistic models. An algorithm for updating the realistic mating constraints, between rigid and nonrigid parts, is developed. The case study of an assembly with planar and cylindrical joints is presented.