In ultra-precision machining (UPM), position-independent geometric errors (PIGEs), i.e., squareness errors, have a crucial impact upon the form accuracy of a machined surface. Accordingly, more research work has been conducted in PIGE identification, to improve the form accuracy. However, the general identification methods were developed without consideration of the specific squareness errors for crucial PIGEs under the form errors of the machining process. Therefore, a new method with featured structures was proposed, to identify crucial PIGEs in UPM. Firstly, a volumetric error model was developed for PIGEs, to discuss the relationship between squareness errors and their resulting machining form errors. Secondly, following the developed model, some featured structures have been proposed with their machining form errors, to significantly indicate crucial PIGEs. Finally, a series of UPM and measuring experiments were conducted for the featured structures, and then their machining form errors were measured and extracted with specific squareness errors for the identification of crucial PIGEs. The theoretical and experimental results revealed that the proposed method is simple and efficient with the featured structures to accurately identify crucial PIGEs in UPM. Significantly, the study offers a deep insight into high-quality fabrication in UPM.