Scanning Electron Microscope (SEM) is a valuable tool for measuring Critical Dimensions (CD) of semiconductor devices at the nanometer scale. Vertical SEM application is one of the applications for high accurate CD measurement on cross-sectional surface. Even a slight stage tilt angle change of the vertical sample can impact CD values in nanometer scales of the sample surface features. For accurate CD measurements, it is essential to ensure the sample is positioned correctly to acquire the sample image. However, it is challenging to achieve a perfect alignment with the incident beam direction and the accurate perpendicular direction on the cross-sectional surface on SEM tool. To achieve an ideal vertical positioning of the sample, the combination of the stage tilt axis and stage rotation axis can be used. Exact calculation is required to achieve an accurate CD measurement. In this paper, a calculation method of the tilt angle correction to achieve a perpendicular angle to the surface and its verification method are described. Reliable measurement can be achieved by employing an automated script for compensation. We also demonstrate an approach for highly reliable angle correction and improved metrology results in this paper.