An auto e-beam tilt technology was used to measure bottom critical dimensions (CD) of High-Aspect Ratio (HAR) contact holes. Results show that traditional Scanning Electron Microscope (SEM) is not capable of catching bottom information, such as bending structures. A new method with hardware and software has been developed to first find the best angle to detect bottom electron signals with high acceleration voltage and then synthesize with multi-angle electron signals. By using this method, accurate bottom CD as well as the angle and direction of bended hole can be measured automatically. It is very effective for inline metrology of HAR 3D structure in semiconductor wafer processing.