Systems and methods for de-identification of medical images can be applied to medical images acquired using various techniques. A 3D medical image can be analyzed to generate an image mask that partitions the image into a foreground region and a background region. From the image mask, a “skin surface” can be reconstructed based on the boundary between the foreground region and the background region. The image mask can be modified, e.g., by moving a randomly-selected subset of the voxels from the foreground region to the background region so that the shape of the skin surface is altered, thus obscuring patient-identifying features. The original medical image can be modified by changing the intensity of voxels in the background region while preserving the original intensity of voxels in the foreground region.