Polymer nanocomposite (PNC) films are of interest for many applications including electronics, energy storage, and advanced coatings. In phase-separating PNCs, the interplay between thermodynamic and kinetic factors governs the assembly of polymer-grafted nanoparticles (NPs), which directly influences material properties. Understanding how processing parameters affect the structure-property relationship of PNCs is important for designing advanced materials. This thesis provides insight by investigating a model PNC system of poly(methyl methacrylate)-grafted nanoparticles (PMMA-NPs) embedded in a poly(styrene-ran-acrylonitrile) (SAN) matrix.Time-of-flight secondary ion mass spectrometry (ToF-SIMS) was developed to quantify the distribution of NPs within PMMA-NP/SAN films, enabling precise 3D reconstruction of PNC structures. Experimental parameters such as primary ion beam angle and charge compensation were optimized to enhance secondary ion signals and depth resolution. Upon annealing in the two-phase region, PMMA-NP/SAN films exhibited phase separation and surface segregation, leading to morphological evolutions characterized by atomic force microscopy (AFM), ToF-SIMS, water contact angle measurements, and transmission electron microscopy. By systematically exploring the effects of film thickness on PNC structures, we found that film thickness-induced confinement reduces lateral phase separation and enhances NP dispersion at the surface. A dimensional crossover from three to two dimensions was observed around 240 nm, below which surface-directed spinodal decomposition is suppressed. As a result of phase separation and surface segregation, six distinct bulk morphologies were identified, allowing for the construction of a morphology map correlating film thickness and annealing time. Among these morphologies, percolated structures were found to improve mechanical properties such as hardness and reduced modulus, as measured using AFM nanoindentation. Notably, interconnected networks show the highest hardness and modulus at both low and high force loadings. Additionally, Marangoni-induced hexagonal honeycomb patterns were observed in spin-coated as-cast PMMA-NP/SAN films. By changing to a less volatile solvent, these defects were eliminated, demonstrating the importance of solvent selection in achieving uniform and high-quality thin films. These findings demonstrate the potential for precise control of surface-enriched and phase-separated microstructures in PNC films through tailoring processing conditions. This thesis advances the understanding of processing-structure-property relationships in PNCs, providing a foundation for designing highly functional materials with broad industrial applications.