We report in this paper simulations for deformed shape predictions of three-dimensional (3-D) microstructures fabricated by the plane pattern to cross-section transfer (PCT) technique and synchrotron radiation (SR) lithography. The investigation of the shape-prediction system enhances the possibility for higher accuracy of the prediction. In addition, the desired shapes can be confirmed by the shape prediction before designing the mask and running experiments. It is necessary to investigate a variety of error factors to shape prediction. We attempted various investigations. One of the possible causes could be the etching direction, which is dependent on the developing time. Therefore, we currently emphasize on the factor causing this error. In order to comprehend the mechanism of the factor, an algorithm that can simulate development was devised. We have developed a mathematical system of X-ray energy distribution onto the PMMA (polymethylmethacrylate) resist, and the shape prediction is consequent to the simulations based on calculations from the mathematics software. The mathematical system for energy distribution depends on the SR light source, X-ray mask specification, and resist specification. As a result, the predicted structures relevant to the absorbed energy–depth–position parameter set and absorbed energy–etching rate parameter set were obtained from this system. This system for shape prediction was implemented by the above parameter sets in C language. Copyright © 2010 Institute of Electrical Engineers of Japan. Published by John Wiley & Sons, Inc.