Systems and methods for optimal electron beam metrology guidance are disclosed. According to certain embodiments, the method may include receiving an acquired image of a sample, determining a set of image parameters based on an analysis of the acquired image, determining a set of model parameters based on the set of image parameters, generating a set of simulated images based on the set of model parameters. The method may further comprise performing measurement of critical dimensions on the set of simulated images and comparing critical dimension measurements with the set of model parameters to provide a set of guidance parameters based on comparison of information from the set of simulated images and the set of model parameters. The method may further comprise receiving auxiliary information associated with target parameters including critical dimension uniformity.