The calculation of heat transfer in systems with large thermal inertia in the time domain is a process that needs high computer capacity and CPU time. This is the case for problems as two or three dimensional heat transfer to the ground when calculating ground heat loss from buildings and different configurations for ground heat storage. Furthermore a finite difference software based on rectangular elements gives an ineffective element structure resulting in an excessive number of elements and elements with an unfavorable aspect ratio. The strategy chosen in the present work is to use standard finite element software which gives the possibility to use triangular elements and to run different physical models in parallel and with interaction between the models. The use of standard finite element codes also gives instant access to advanced features of pre- and post-processing. From earlier work the formulation of the solution for the heat transfer equation in the for a given in the frequency domain gives the possibility to formulate the problem as two steady state temperature fields, one for the real and one for the imaginary parts of the temperature oscillation. The different temperature fields are interlinked via the heat source term. In this way the solution time for each frequency will be of the same order of magnitude as for the steady state solution. The modern finite element software gives the user the possibility to create macros or scripts for administration of calculations giving the possibility within the software environment to convert real time data into Fourier series, run the solution for a large set of frequencies and to carry out the inverse transformation of the results to time series. In this way a rational and highly effective calculation technique for this problem area can be reached. The use of the technique is demonstrated for simulation of annual heat and moisture balance for a crawlspace, for building heat loss to the ground and for ground heat storage.