Abstract: In the fields of micro/nano positioning application, error analysis is an effective way to enhance the precision of such micromanipulators. Manufacturing imperfections, which are inevitable, are the most important factors influencing the accuracy. Thus, various manufacturing errors were studied by taking a planar 3-DOF(degree of freedom) flexure hinge-based micro robot as a case. By means of formulating static stiffness of the robot, mapping between manufacturing imperfections and end-effector positioning accuracy was obtained. Based on theoretical calculation and finite element method, effects of various machining imperfection types on end-effector positioning accuracy were evaluated. The results show that errors of the radius of the hinges and angular differences of the center line of the hinges are dominant factors resulting in output errors. Conclusions drawn from experiments can instruct the design of compliant parallel mechanisms by distributing various configurable parameters’ manufacturing differences to ensure the output precision of the end effector within required range; they may also be helpful while calibrating this kind of manipulators.