The paper describes about a useful study on the deformed shapes of microstructures fabricated by PCT (Plane-pattern to Cross-section Transfer) Technique. Previously, we have introduced the PCT technique as an additional process to conventional X-ray lithography for an extension of 2.5-dimensional structure to 3-dimensional structure. The PMMA (poly-methylmethacrylate) has been used as the X-ray resist. So far, microneedle and microlens arrays have been successfully fabricated in various shapes and dimensions. The production cost of X-ray mask has been known as the most expensive process for LIGA step, therefore, to predict the resulting shapes of structure precisely before fabricating the mask is relatively important. Although, the 2-D pattern on the X-ray mask can form a similar shape resulting in 3-D structure, the distorted shapes of microstructures have been observed. A linear-edged pattern on the X-ray mask resulted as an exponential-edged structure and an exponential-edged pattern resulted as an exceeding curvature, for example. This problem causes a change in the functional property of the array. In the case of our microneedle array, the linear-edge is highly required since it increases the strength of microneedle. We have investigated and suggested a calculation method fir a shape-prediction of microstructure fabricated by PCT technique in this work. The compensation calculation by our theories for an X-ray mask design can solve the undesired shape resulting after X-ray exposure. Moreover, the dosage control and suitable developing time are given in order to see through the current condition of the currently used synchrotron radiation light-source.