Mechanical thinning of Si die backside was introduced to support fault isolation for flip chip package in this paper. The backside milling system provides two types of thinning with good die planarity and mirror polishing to yield a high image quality for fault isolation techniques such as laser base thermal emission and photon emission techniques. In this paper, two mechanical thinning techniques were applied by using the 3D die curvature thinning and 2D planar thinning on flip chip Si backside. The impact of process parameters on die planarity and fault isolation were also discussed. The experimental results demonstrate the milling system’s high uniformity across the large die size and provide a very good solution for fault isolation techniques.