The concept of Skin Model Shapes has been proposed as a method to generate digital twins of manufactured parts and is a new paradigm in the design and manufacturing industry. Skin Model Shapes use discrete surface representation schemes, such as meshes and point clouds, to represent surfaces, which makes them enablers to perform an accurate tolerance analysis and surface inspection. However, online inspection of manufactured parts through use of Skin Model Shapes has not been extensively studied. Moreover, the existing geometric variation inspection techniques do not detect unfamiliar changes within tolerance, which could be the precursors to the onset of the manufacturing of out of tolerance part. To detect the unfamiliar changes, as anomalies, and categorize them as systematic and random variations, some unique surface characteristics can be extracted and studied. Random surface deviations exhibit narrow normal distributions, and systematic deviations, on the other hand, exhibit wide, skewed, and multimodal distributions. Using those surface characteristics as key traits, machine learning classifiers can be used to classify deviations into systematic and random variations. To illustrate the method, multiple samples from a truck component manufacturing line were scanned and the collected 3D point cloud data was used to extract features. A prediction score of 97-100% can be achieved by decision tree, k-nearest neighbor, support vector machines, and ensemble classifiers. The purposed approach is expected to extend the existing online inspection approaches and applications of Skin Model Shapes in quality control.