The nanotechnology has emerged as an effective tool to fabricate next-generation microelectronics, biologically responsive materials, and structured membranes. The self-assembly of nanoscale phases has extensively been studied in thin films because of their potential applications in sub-100 nm structures. The control of the ordering of nanaoscale patterns is critical for various technological applications. A variety of approaches such as topographical and chemical patterning have resulted in an enhancement in long-range orders of nanoscale patterns. The macroscopically large areas of nanoscale domains with single-crystal order in polymer thin films can be utilized to fabricate portable ultra-high density data storages, advanced sensors and ultra-light electronic devices. However, as pattern size decreases below 100 nm, there appear many new challenges such as the cost of patterning and the precise control of the line edge roughness and line width roughness. Precisely controlling nanostructure shapes and placements in material is a continuing challenge. Measurement platform to provide accurate and detailed information about nanostructure orientations and placements is a key to this challenge. In this review, we examine the recent progress of characterization tools in polymer thin films. We highlight our efforts to control surface pattern formations of polymer thin films and our use of statistically-useful scattering techniques and real-space imaging tools to quantify the order of nanoscale patterns. In some technological applications of biological membranes, such as chemical separations, drug delivery and sensors, the orientation distribution of nanostructures is often more important. The real-space imaging methods of characterizing the orientation distribution of nanostructures, such as cross-sectional electron microscopy measurements and depth profiling by alternating etch and surface imaging steps are readily performed on thin polymer films over large areas. However, these real-space imaging techniques are destructive measures of nanostructures in polymer thin films. Also it is challenging to in-situ measure the evolution of orientation of nanoscale patterns during processing by using these destructive real-space imaging techniques. Rotational small-angle neutron scattering (RSANS) and grazing-incidence small-angle x-ray scattering (GISAXS) are effective and non-destructive measurement tools to measure the evolution of orientation distribution of nanoscale patterns during processing. In this rotational small angle neutron scattering method, the sample is rotated in the neuron beam. By accumulating the scattering density at each sample rotation angle, the three-dimensional Fourier space of the internal ordering in the nanostructured film can be mapped. By using this relatively new rotational small angle neutron scattering method and established models for nanoscale patterns, the full three-dimensional orientation distribution of nanoscale patterns can be obtained.