Modern electronic devices will be based on complex nanometer scale materials structures, and biological and chemical sensors will employ multifunctional nanostructures that integrate molecular, biological and electronic materials. It is only recently that techniques have been developed to image the dynamics of nanometer scale structures and to determine their properties. Our group has applied advanced microscopy and spectroscopy techniques to characterize the growth and properties of thin film interfaces and nanostructures. We have led the developent of photo electron emission microscopy (PEEM) with tunable UV light from a free electron laser. Our students have explored the dynamics and interactions of nanostructures as they grow or evolve. Scanning probe systems have also been used as a basis for imaging polar materials including ferroelectric materials and wurtzite structured semiconducting materials such as GaN. These techniques offer the possibility to develop nanopatterning approaches that can drive self assembly of molecular, biological and electronic nanostructures.