This article provides an estimation model for calibrating the kinematics of manipulators with a parallel geometrical structure. Parameter estimation for serial link manipulators is well developed, but fail for most structures with parallel actuators, because the forward kinematics is usually not analytically available for these. We extend parameter estimation to such parallel structures by developing an estimation method where errors in kinematical parameters are linearly related to errors in the tool pose, expressed through the inverse kinematics, which is usually well known. The method is based on the work done to calibrate the MultiCraft robot. This robot has five linear actuators built in parallel around a passive serial arm, thus making up a two-layered parallel-serial manipulator, and the unique MultiCraft construction is reviewed. Due to the passive serial arm, for this robot conventional serial calibration must be combined with estimation of the parameters in the parallel actuator structure. The developed kinematic calibration method is verified through simulations with realistic data and real robot kinematics, taking the MultiCraft manipulator as the case.