This presentation will focus on an examination of the dynamical properties and self-organizing behavior of thin films spanning 2D molecular systems through nano-confined 3D polymeric films. Such information can be extracted successfully from the powerful combination of surface-sensitive atomic beam scattering coupled with real-time/real-space variable-temperature scanning probe imaging to visualize local events on atomic and nano length-scales. The organizational dynamics of diblock copolymers in thin films as well as under nanoconfinementwill be discussed. Specific topics will include real-time/real-space visualization of defect mobility, fluctuations and annihilation, phase separation, and the spatial control of degenerate structures in intentionally created nanostructures via the application of electric fields. Such phase-separated diblock copolymers have attracted much fundamental and technological interest due to their ability to act as templates for the bottom-up formation of metallic, molecular, and nanoparticle arrays with high lateral spatial definition. For example, we are using such substrates to guide the formation of highly aligned arrays of gold nanorods that we have recently shown to be highly efficacious SERS substrates. The presentation will also discuss the application of molecular beam gas-surface scattering methods to probe the dynamical properties of polymeric interfaces, including the effect of nanoconfinement on polymer chain dynamics, the interfacial properties of thin films in their glassy versus crystalline phases, and the general issue of collisional energy exchange involving complex interfaces. This will extend to molecular interfaces, including methylated silicon, which is a new and important technological interface due to its superior oxidative and electrochemical stability relative to hydrogen-terminated silicon. Our results here will examine the structure and surface phonon dynamics of (1x1) CH3- and CD3-terminated Si(111), giving precise details of how adlayer librations couple with the phonon structure of the underlying semiconductor. Time permitting, closing remarks will survey recent work from our group on energetic embedding of molecules into ice, and the isolation of reaction intermediates during the oxidation of unsaturated SAMs.