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This paper describes the alignment automation of nanotools and nanoparts inside the vacuum chamber of a scanning electron microscope (SEM). As nanopart example carbon nanotubes have been selected and as a nanotool a tip of a scanning tunneling microscope has been chosen. The experimental setup and its control architecture are shown. Different microrobots and sensors can be integrated in a flexible manner using a common control interface within this architecture. The system easily scales up for more complex robot and sensor setups. An automation sequence is proposed and experimental data is evaluated.