Probing nanometer-sized structures to evaluate the performance of integrated circuits (IC) for design verification and manufacturing quality monitoring demands precision nanomanipulation technologies. To minimize electron-induced damage and improve measurement accuracy, scanning electron microscopy (SEM) imaging parameters must be cautiously chosen to ensure low electron energy and dosage. This results in significant image noise and drift. This paper presents automated nanoprobing with a nanomanipulation system inside a standard SEM. We achieved SEM image denoising and drift compensation in real time. This capability is necessary for achieving robust visual tracking and servo control of nanomanipulators for probing nanostructures in automated operation. This capability also proves highly useful to conventional manual operation by rendering real-time SEM images that have little noise and drift. The automated system probed nanostructures on an SEM metrology chip as surrogates of electronic features on IC chips. Success rates in visual tracking and Z-contact detection under various imaging conditions were quantitatively discussed. The experimental results demonstrate the system's capability for automated probing of nanostructures under IC-chip-probing relevant electron microscope imaging conditions.