In modelling flexure based mechanisms, generally flexures are modelled perfectly aligned and nominal values are assumed for the dimensions. To test the validity of these assumptions for a two Degrees Of Freedom (DOF) large stroke compliant mechanism, eigenfrequency and mode shape measurements are compared to results obtained with a flexible multibody model. The mechanism consists of eleven cross flexures and seven interconnecting bodies. From the measurements 30% lower eigenfrequencies are observed than those obtained with the model. With a simplified model, it is demonstrated that these differences can be attributed to wrongly assumed leaf spring thickness and misalignment of the leaf springs in the cross flexures. These manufacturing tolerances thus significantly affect the behaviour of the two DOF mechanism, even though it was designed using the exact constraint design principle. This design principle avoids overconstraints to limit internal stresses due to manufacturing tolerances, yet this paper shows clearly that manufacturing imperfections can still result in significantly different dynamic behaviour.