Climate data are hardly available in remote areas like high arctic permafrost regions. Upscaling of climate processes becomes therefore an essential element in predicting the impacts of changing climate conditions.Methods for upscaling the major energy exchange processes between ground and atmosphere in permafrost regions are developed within the HGF-Project: Sensitivity of permafrost systems water and energy balance under changing climate: A multiscale perspective (SPARC). The project includes the important aspect of changing surface characteristics and their impact on permafrost energy balance. Field works for this purpose took place in July and August 2007 on the island Samoylov in the center of the Lena-River-Delta. The focus of this work rests upon energy balance variation within polygonal structures, which are the most dominant surface elements of this region. Surface properties of two typical polygons in different development stages are considered under the aspect of energy exchange processes between soil and atmosphere. This includes a more general analysis of the thermal properties of specific vegetation units in association with micro relief and moisture content. For evaluating inter polygonal energy balance variations, climate data have to be measured in a very high spatial resolution. Standard climate stations usually record temporal variations of energy balance on point scale. They are not able to provide information about spatial variations. This problem is sometimes bypassed by using multiple or mobile climate stations. However this generally results in very coarse data of spatial differences. Thus a climate station has been modified to a 10m long scanner system for getting a more detailed picture of the spatial energy balance variations between the chosen polygon types. This system allows the record of spatial variations in combination with high frequent measurements of a standard climate station.The scanner system measures short and long wave radiation balance, reflected photosynthetic active radiation, air temperature and humidity in 70 cm height. Variables like air temperature and humidity in 2 m height, as well as air pressure and wind speed that are not supposed to change significant along the running way are measured in a common manner. Soil temperature and moisture sensors where installed underneath the scanner track.The scanner technique gives a more detailed picture of the relation between energy fluxes and surface structures. The results will be used to close the gap between point based and spatial climate models. They also enhance the potentials of remote sensing data when surface information is related to energy fluxes.