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A major impediment to the development of physics-based multi-scale homogenization (composite) theories is the lack of appropriate methods to characterize the local anisotropic elastic-plastic properties of microscale constituents and interfaces at various hierarchical length scales in composite material systems. This work aims to address this gap by combining the information obtained from spherical nanoindentation with different indenter sizes, structure characterization methods (e.g., Orientation Image Mapping in Scanning Electron Microscope, X-ray microtomography),and sophisticated finite element models to arrive at reliable estimates of the elusive local properties. The methods developed have been critically validated in a series of material systems with increasingly complex internal structures, starting with single-phase cubic and hexagonal metals and progressing to multi-phase metals, freeze-cast polymer-ceramic composite systems with novel but highly complex hierarchical internal structures, and various biomaterials. Using these novel approaches, we were able to quantify reliably for the first time the local mechanical properties exhibited by various microscale constituents and interfaces.