In this paper, the authors are showing the organizational and technical challenged encountered while preserving wooden architecture in the Carpathian region. The authors are presenting two case studies of 3D scanning of wooden churches in Romania and Poland, which were performed using terrestrial laser scanning (TLS) and terrestrial short-range photogrammetry (TSRP). The paper describes the workflow of the operation, challenges during scanning due to both organization, technology limitations, access to the buildings and even weather, and solutions applied during the process of digitalization of these historical buildings.