Abstract A hyperspectral sensor is able to acquire the physical and optical properties of surfaces. On the other hand, applications in climate research, ecology, cultural heritage, and industry require metrological solutions for diagnosis and control quality. Thus there is a direct relationship between the physical properties of materials and their processing results obtained from spectral measurements. Two types of measurements are considered. First, each material of interest can be identified or modeled through a single spectrum. The second type considers that a material does not present a uniform response. Therefore its identification can be done through the distribution of its spectra. In order to preserve the metrological properties of the acquired measurements while also solving the “curse of dimensionality” problem, these considerations are expressed in the domain of spectral differences. Protocols to assess the metrological properties of difference functions are provided, along with applications in remote sensing data analysis.