Abstract Scanning electron microscope (SEM) and high resolution transmission electron microscope analysis combined with focused ion beam have been used to locate the physical defect. Visualizing the defect by these techniques was found to be difficult. This paper introduces a novel physical failure analysis technique using 3D rotation STEM imaging. It describes the electrical method of analyzing the cause of failure. Trying to determine with 2D imaging if the defect was a crystalline or not was problematical. To resolve the issue, a pillar type of specimen was made by utilizing a 3D rotation holder and observed with the sample from different directions. Results confirmed that the generation of dislocations can occur according to the variation of the stress transferred to the bulk Si. The variation was due to stress intensity and pattern isolation as a function of the film volume of spin on dielectric material and shallow trench isolation size.