The realistic modeling of assemblies’ parts with manufacturing deviations during the tolerancing process is an important task for designers. In Computer Aided Design (CAD), several methods are proposed for the tolerancing of mechanical products considering different type of defects such as dimensional and geometrical errors. However, form defects are neglected or modeled using complex theoretical approaches during the evaluation of the realistic product operation. In this regard, this paper investigates CAD-based modeling of cylindrical components with form defects in tolerancing context. A CAD method based on the B-spline interpolation is developed to reconstruct realistic cylindrical parts with form defects. New algorithms for updating the mating constraints especially between realistic rigid parts with form defects are highlighted. In fact, new automated sub-algorithms are used to redefine the mechanical parts joints, while respecting the Objective Function of the Assembly (OFA). The proposed method allows representing cylindrical parts and assemblies with form deviations in the Digital Mock-Up (DMU) considering the perturbed points of the discretized geometry according to form tolerances types and values.