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After constructing a grid-based 3D surface model (GSM) for a customized cushion seat using stereo visions, we have observed that the model needs to be manually edited for minimizing the ridges. This paper presents a systematical approach to develop a visual manipulation tool, called VT-GSM, for visually manipulating GSMs. To realize the approach, a 3D graphic transformation pipeline has been adopted and modified, and then, incorporated with the pipeline, a Model-View-Controller pattern has been applied for designing the architecture of the VT-GSM. After that, a variety of operations have been proposed, implemented, and demonstrated for manipulating GSMs. Finally, a polished cushion seat model has been illustrated using the VT-GSM.