Continuous phase plates (CPPs) are increasingly being used to realize beam shaping and smoothing in high-power laser systems. With computer controlled optical surfacing (CCOS) technology, CPPs can be imprinted with high accuracy by a series of processing iterations, in which the characterization of the imprinted CPP surface plays a key role. However, the form accuracy evaluation is sensitive to the misalignment caused by the difference between the designed and measured coordinates. In this paper, the matching problem, which is the critical part of characterization, is first summarized as a least squares problem in accordance with the processing principle of CPPs. Then, the misalignment effect on the form error evaluation is analyzed. Necessary attention is paid to the CPP features and the sensibility analysis for different misalignments is conducted. To improve the efficiency and accuracy, an automatic characterization method based on image registration and nonlinear optimization is presented. Considering the smoothness of the CPP surface, the height difference tracing method is proposed to evaluate the matching performance and embedded into the characterization method. Finally, a series of simulations and experiments were undertaken to verify the performance of the proposed characterization method. The results demonstrated the feasibility of the proposed method, indicating that it can provide the reliable form error evaluation with sub-nanometer accuracy for imprinted CPPs.