Nanoparticles are essential for energy storage, catalysis, and medical applications, emphasizing their accurate chemical characterization. However, atom probe tomography (APT) of nanoparticles sandwiched at the interface between an encapsulating film and a substrate poses difficulties. Poor adhesion at the film-substrate interface can cause specimen fracture during APT, while impurities may introduce additional peaks in the mass spectra. We demonstrate preparing APT specimens with strong adhesion between nanoparticles and film/substrate matrices for successful analysis. Copper nanoparticles were encapsulated at the interface between nickel film and cobalt substrate using electrodeposition. Cobalt and nickel were chosen to match their evaporation fields with copper, minimizing peak overlaps and aiding nanoparticle localization. Copper nanoparticles were deposited via magnetron sputter inert gas condensation with varying deposition times to yield suitable surface coverages, followed by encapsulation with the nickel film. In-plane and cross-plane APT specimens were prepared by femtosecond laser ablation and focused ion beam milling. Longer deposition times resulted in agglomerated nanoparticles as well as pores and voids, causing poor adhesion and specimen failure. In contrast, shorter deposition times provided sufficient surface coverage, ensuring strong adhesion and reducing void formation. This study emphasizes controlled surface coverage for reliable APT analysis, offering insights into nanoparticle chemistry.