In this study, registration methods used to estimate both position and orientation differences between two images had been evaluated. This is an important issue since that there are always some position and orientation differences when loading test samples on the inspection machine. These differences should be calculated and compensated before further analysis. Registration methods tested including one area method and three feature based method. It was shown that the area method had better performance than other feature based method in these cases studied. And it is shown that it is much easy to detect defect by analyzing the subtracted image with position and orientation compensation instead of those without compensation.