The atomic force microscopy (AFM) technology is a promising method for nanofabrication due to the high tunability of this affordable platform. The quality inspection and control significantly impact the manufacturing effectiveness for realizing the functionality of the achieved nanochannel. Particularly, the surface characteristics of nanochannel sidewalls, which play a significant role in determining the quality of the nanomachined products, can not be accurately captured using conventional surface integrity metrics (e.g., surface roughness). Therefore, it is necessary to propose a method to quantitatively characterize the surface morphology and detect the abnormal parts/regions of the nanochannel sidewall. This paper presents a statistical process control approach derived from the self-affine fractal model to detect the sidewall surface anomalies. It evaluates changes in the self-affine fractal model parameters (standard deviation, correlation length, and roughness exponent), which can be used to signify the changes on the sidewall surface; the statistical distributions of these parameters are derived and used to develop control charts to allow inspection of the sidewall morphology. The approach was tested on the AFM-based nanomachined samples. The results suggest that the presented approach can effectively reflect the abnormal regions on the machined parts, which opens up a new avenue toward guiding the quality control and rework for process improvement for AFM-based nanomachining.