A method and system for inspecting a customized orthodontic aligner for manufacturing defects are described. The method includes obtaining images of the customized orthodontic aligner, determining a digital file associated with the aligner, the digital file including a digital model of a mold used during manufacture of the customized orthodontic aligner, determining an inspection recipe for the aligner, determining an intended property for the customized orthodontic aligner by digitally manipulating the digital model of the mold, determining an actual property of the customized orthodontic aligner from the images, determining whether there is a manufacturing defect in the customized orthodontic aligner by comparing the intended property with the actual property, and outputting an output associated with the determination of whether there is a manufacturing defect.