Nanocomposite membrane assemblies are a class of materials that incorporate inorganic/organic nanoscale materials, such as fullerenes and gold nanoparticles or nanostructured materials with bio-inspired amphiphilic structures composed of molecules such as lipids or block copolymers. One of the intrigues of such materials is the potential to develop programmable membrane assemblies that mimic biological membrane complexity, dynamics and function. Due to the nanoscale nature of the assemblies, it becomes necessary to understand interactions between these materials with nanoscale resolution. Although many techniques are able to provide information as to the overall organization of membrane-based assemblies, only scanning probe microscopy (SPM) methods allow for a direct visualization of stochastic processes under environmentally relevant conditions. Here, an overview of nanocomposite membrane and thin film architecture investigations is presented with an emphasis on using in situ atomic force microscopy (AFM) in combination with fluorescence microscopy/spectroscopy techniques to understand organization and dynamics, in relation to activities and capabilities at the Center for Integrated Nanotechnologies.