A method for preparing a sample for transmission electron microscopy (TEM) comprises providing a substrate having a patterned area on its surface that is defined by a particular topography. A conformal layer of contrasting material is deposited on the topography by depositing a layer of the contrasting material on a local target area of the substrate, spaced apart from the patterned area via Electron Beam Induced Deposition (EBID). The deposition parameters, the thickness of the layer deposited in the target area, and the distance of the target area to the patterned area are selected so that a conformal layer of the contrasting material is formed on the topography of the patterned area. A protective layer is subsequently deposited. The protective layer does not damage the topography in the patterned area because the patterned area is protected by the conformal layer.