Electron microscope tomography [1] has been proven as an essential technique for imaging the structure of cells beyond the range of the light microscope down to the molecular level. However, because of the extreme difference in spatial scales, there is a large gap to be bridged between light and electron microscopy. Various techniques have been developed, including increasing size of the sensor arrays, serial sectioning and montaging. Data sets and reconstructions obtained by the latter techniques generate many 3D reconstructions that need to be glued together to provide information at a larger spatial scale. However, during the course of data acquisition, thin slices may become warped in optical and electron microscope preparations. We review some procedures for de-warping sections and reassembling them into larger reconstructions, and present some data from electron microscopy.