Nanostructure interactions contribute strongly to structure uniformity and defect formation. Characterizing the interaction not only assists to understand the growth kinetics but also provides a metric to benchmark growth quality. Chapter 15 presented interaction modeling and estimation methods for one local region, which assume complete feature measurement. In order to map interaction patterns across the whole substrate, direct application of the methods would require complete information of a specimen. This implies a formidable metrology task using current inspection techniques such as scanning electron microscopy (SEM). In this chapter, we relax the metrology constraint and analyze nanostructure interactions with incomplete feature measurement. Specifically, we optimize Expectation-Maximization (EM) algorithm based on Markovian properties of interaction modeling and develop a tailored space filling design to select which sites to measure.