The strength estimation of built-in historical timber requires extensive investigation of internal wooden structures and properties, which cannot be mapped using only optical surveying methods. In most cases, additional equipment is required, including invasive techniques such as drilling resistance technology and sensitive methods such as ultrasonics or electromagnetic (EM) sensor technology. Thus, the localisation of a measuring device within a whole timber structure and the uniform registration of internal and external wooden structures is missing. In this article, we investigate the capability to localise the EM sensor, which will be used in future research activities for in-depth analysis of internal timber structures. The position of the EM sensor will be captured during the 3D timber imaging using different optical methods to provide a reference between the external wood surface and digitised internal structures. The data quality is compared and evaluated according to the measurement method using geometric features and visual expertise.