The interactions between nanoparticles and rough Surfaces are of great scientific and engineering importance and have numerous applications in surface science and biotechnology. Surface geometry and roughness play crucial roles in observed particle adhesion forces. We previously developed a model and simulation approach to describe adhesion between microscale bodies. This work provides detailed descriptions of the modeling framework, with associated experimental validation, applied to nanoscale systems. The physical systems of interest include nanoscale silicon nitride adhering to different surfaces in both dry and aqueous environments. To perform the modeling work, precise descriptions of the geometry of the particle and the roughness of the particle and substrate were generated. By superimposing the roughness and geometry models for the particle and the substrate, it was possible to precisely describe the spatial configurations of the adhering surfaces. The interacting surfaces were then discretized, and the adhesion force between the two surfaces was calculated by using Hamaker's additive approach, based on van der Waals interactions. In the experimental work, an atomic force microscope (AFM) was used to measure the adhesion force (pull-off force) between nanoscale silicon nitride cantilever tips and a range of substrates in different environments. The measured and predicted force distributions were compared, and good agreement was observed between theory and experiment.