Methods and apparatus are disclosed for forming a sample of an object, extracting the sample from the object, and subjecting this sample to microanalysis including surface analysis and electron transparency analysis in a vacuum chamber. In some embodiments, a method is provided for imaging an object cross section surface of an extracted sample. Optionally, the sample is iteratively thinned and imaged within the vacuum chamber. In some embodiments, the sample is situated on a sample support including an optional aperture. Optionally, the sample is situated on a surface of the sample support such that the object cross section surface is substantially parallel to the surface of the sample support. Once mounted on the sample support, the sample is either subjected to microanalysis in the vacuum chamber, or loaded onto a loading station. In some embodiments, the sample is imaged with an electron beam substantially normally incident to the object cross section surface.