This paper addresses the problem of object-mask registration, which aligns a shape mask to a target object instance. Prior work typically formulate the problem as an object segmentation task with mask prior, which is challenging to solve. In this work, we take a transformation based approach that predicts a 2D non-rigid spatial transform and warps the shape mask onto the target object. In particular, we propose a deep spatial transformer network that learns free-form deformations (FFDs) to non-rigidly warp the shape mask based on a multi-level dual mask feature pooling strategy. The FFD transforms are based on B-splines and parameterized by the offsets of predefined control points, which are differentiable. Therefore, we are able to train the entire network in an end-to-end manner based on L2 matching loss. We evaluate our FFD network on a challenging object-mask alignment task, which aims to refine a set of object segment proposals, and our approach achieves the state-of-the-art performance on the Cityscapes, the PASCAL VOC and the MSCOCO datasets.