Light-matter interplay is widely used for analyzing the topology of surfaces on small scales for use in areas such as nanotechnology, nanoelectronics, photonics, and advanced materials. Conventional optical microscope imaging methods are limited in resolution to a value comparable to the wavelength, the so-called Abbe limit, and cannot be used to measure nano-sized structures. Scatterometry and Mueller ellipsometry are spectroscopic optical methods that can measure structures smaller than the wavelength. However, the relative uncertainties of the structure dimensions measured with scatterometry increase with decreasing structure size, and the industry is therefore replacing simple intensity based scatterometry with Mueller ellipsometry for the most demanding measurements. The accuracy of Mueller ellipsometry and scatterometry are closely related to the ability of the employed regression and regularization algorithms to extract the structural dimension. In this work, we demonstrate how the measurement accuracy on three-dimensional periodic structures may be increased by measuring the same periodic structure with multiple techniques and applying a χ2-regression method that finds the best solution based on the input from all the instruments. We furthermore report on a new and improved calibration method for Mueller ellipsometry and demonstrate how the Mueller matrix may be used to find the geometrical anisotropy of the structure.