Quantification of very low density molecular coatings on large (60 nm) gold nanoparticles (AuNPs) is demonstrated via the use of antibody-mediated self-limiting self-assembly of small and large AuNPs into raspberry-like structures subsequently imaged by atomic force microscopy (AFM). AFM imaging is proposed as an automated, lower-cost, higher-throughput alternative to immunostaining and imaging by transmission electron microscopy. Synthesis of large AuNPs, containing one of three ligand molecules in one of three stoichiometries (1, 2, or 10 ligands per AuNP), and small probe AuNPs with one of three antibody molecules in a one antibody per AuNP ratio, enabled a range of predicted self-limiting self-assembled structures. A model predicting the probability of observing a given small to large AuNP ratio based on a topography measurement such as AFM is described, in which random orientational deposition is assumed and which accounts for the stochastic synthesis method of the library AuNPs with varied ligand ratios. Experimental data were found to agree very well with the predictive models when using an established AFM sample preparation method that avoids drying-induced aggregation.