For automating deburring of cast parts, this paper proposes a general method for estimating burr height using 3D vision sensor that is robust to missing data in the scans and sensor noise. Specifically, we present a novel data-driven method that learns features that can be used to align clean CAD models from a workpiece database to the noisy and incomplete geometry of a RGBD scan. Using the learned features with Random sample consensus (RANSAC) for CAD to scan registration, learned features improve registration result as compared to traditional approaches by (translation error (Δ18.47 mm) and rotation error(Δ43∘)) and accuracy(35%) respectively. Furthermore, a 3D-vision based automatic burr detection and height estimation technique is presented. The estimated burr heights were verified and compared with measurements from a high resolution industrial CT scanning machine. Together with registration, our burr height estimation approach is able to estimate burr height similar to high resolution CT scans with Z-statistic value (z=0.279).