Nanomanipulation inside electron microscopes enables a multitude of precision applications. The semiconductor industry employs this capability to probe sub-micrometer-sized features to evaluate the performance of integrated circuits (IC) for design/quality monitoring. In electron microscopy imaging, the use of low accelerating voltages and high magnifications, as required for IC nanoprobing tasks, results in significant image noise and drift. This paper presents automated nanoprobing with a nanomanipulation system inside a standard scanning electron microscope (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 nanoprobes 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 ICchip-probing relevant EM imaging conditions.