This article presents a computationally intensive adaptive trajectory tracking control algorithm for dynamic control of nanopositioning and nanomeasuring machines. To realize the required high sample rate of the control algorithm, an embedded multiprocessor architecture has been chosen as development target. The model-oriented development approach studied here aims to narrow the gap between the control system design environment MATLAB/Simulink and the actual distributed implementation on the custom platform by introducing a custom code generation target intending the utilization of automatic code generation facilities.