In this paper we show how to obtain a three-dimensional model of virus-infected cells by serial sectioning of resin embedded samples and transmission electron microscopic imaging. The method bases on sample fixation by high pressure freezing and processing by freeze substitution with the goal to preserve the structures of interest close to the natural state, as previously described (Walther et al., High pressure freezing for scanning transmission electron tomography analysis of cellular organelles. In: Mossman BT, Taatjes DJ (eds) Cell imaging techniques, vol 931, Methods in molecular biology. Humana Press, Totowa, NJ, pp 525-535, 2013). Advantages of serial sectioning compared to that of other tomographic methods are as follows: No special and expensive additional equipment is required. Relatively large volumes, such as whole cells, can be three-dimensionally reconstructed in a reasonable amount of time. Serial sectioning is a non-destructive method; the sections can be stored, re-imaged, or processed for immunogold labeling when more specific data are requested or when new scientific questions are raised (e.g., higher magnifications, protein distributions). We have recently used this method to obtain a three-dimensional model of the complete assembly complex of an HCMV infected cell, which allowed a detailed insight into this virally induced compartment (Schauflinger et al., Cell Microbiol 15(2):305-314, 2013).