The structure of a freeze-dried material is essential for its ability to preserve and protect biologics such as proteins, cells and other sensitive structures. The structure of a typical freeze-dried matrix can be described as pores surrounded by thin walls where the walls are the encapsulating material (for e.g. cells). The objective of this investigation is to evaluate X-ray microtomography (µCT) as a characterization method to quantifying the matrix of a freeze dried material, and compare it to scanning electron microscopy (SEM). The material consists of maltodextrin, freeze-dried below or above the glass transition temperature of the maximal freeze concentration (Tg′) and after applying annealing. The SEM images have high resolution and provide an excellent view of the sample. However, it is challenging to perform any image analysis and to ensure that a representative section is presented. The µCT images provide a rather uniform contrast between material and void, allowing for a simple grey-level thresholding when separating structure from the background. A robust image analysis procedure allows the results extracted from a representative sample volume to be evaluated. Further image analysis has been focused on understanding the thickness of the encapsulating structures by estimations of volume-weighted averages of inscribed spheres within the walls. The results show two types of structures: A large pore structure of around 20–100 µm separated by thin walls around 2–3 µm thick, and a finer structure consisting of smaller pockets of air (< 10 µm) packed in a honeycomb like structure. The structures of the samples dried below and above Tg′ have smaller and thinner structures, while material dried after annealing has larger and thicker structures. The structures display comparably small differences between the different drying protocols despite the quite different drying conditions.