Milling of thin-walled aerospace structures is a critical process due to the high flexibility of the workpiece. Current practices in the fixture design and the choice of cutting parameters rely solely on conservative guidelines and the designer’s experience. This is a result of the lack of computationally efficient dynamic models to represent the dynamic response of the workpiece during machining, and the interaction between the workpiece, fixture and the cutting forces. This paper presents a novel dynamic formulation of typical thin-walled pockets encountered in aerospace structures. It is based on an analytical description of a five-sided pocket using a plate model. An off-line calibration of the model parameters, using global and local optimization, is performed in order to match the dynamic response of the pocket structure. The developed simplified model is based on Rayleigh’s energy method. Various pocket shapes are examined under different loading conditions and compared to finite element (FE) predictions and experimental results. In both cases, the results obtained by the developed model are in excellent agreement. This proposed approach resulted in one to two orders of magnitude reduction in computational time when compared to FE models, with a prediction error less than 10%.