To satisfy the increasingly demanding requirements in throughput and accuracy, more lightweight structures and a higher control bandwidth are highly desirable in next-generation motion stages. However, these requirements lead to a more flexible deformation, causing the estimation accuracy of the point of interest (POI) displacement to be guaranteed under the rigid-body assumption. In this study, a soft sensor model is constructed using a dynamic neural network (DNN) to estimate the POI displacement. This model can reflect the dynamic characteristics of the POI and realize accurate estimations. Moreover, a method combining stepwise and weight methods is proposed to analyze the influence of different DNNs, and a performance measure is presented to evaluate the soft sensor model. In the simulation, the DNN with the hidden feedbacks is proved to be the most suitable soft sensor model. The relative error and correlation coefficient obtained were less than 2% and 0.9998, respectively, during training and 5% and 0.9989, respectively, during testing. Compared with the data-driven model using the least-squares method, the proposed method exhibits a higher precision, and the relative error is within the setting range using the proposed performance measure.