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The atomic force microscope (AFM)-based nanomachining has the potential for highly customized nanofabrication due to its low cost and tunability. However, the low productivity and issues related to the quality assurance for AFM-based nanomachining impede it from large-scale production due to the extensive experimental study for turning process parameters with time-consuming offline characterizations. This work reports an analytic approach to capturing the AE spectral frequency responses from the nanopatterning process using vibration-assisted AFM-based nanomachining. The experimental case study suggests the presented approach allows characterizations of subtle variations on the AE frequency responses during the nanomachining processes (with overall 93% accuracy), which opens up the chance to explain the variations of the nano-dynamics using the senor-based monitoring approach for vibration-assisted AFM-based nanomachining.