A substrate (1) is provided comprising on its surface a patterned area (8) defined by a given topography. The substrate is to be processed for obtaining a TEM sample (4) in the form of a slice of the substrate . According to the method of the invention, a conformal layer (7) of contrasting material is deposited on the topography, by depositing a layer (5) of the contrasting material on a local target area (6) of the substrate, spaced apart from the patterned area (8). The material is deposited by Electron Beam Induced Deposition (EBID). The deposition parameters, the thickness of the layer (5) deposited in the target area (6), and the distance of said target area to the patterned area, are such that a conformal layer (7) of the contrasting material is formed on the topography of the patterned area (8). This is followed by the deposition of the protective layer (10), which does not damage the topography in the patterned area (8), as it is protected by the conformal layer (7). The TEM sample (4) is prepared in a manner known in the prior art, for example by FIB. The conformal contrasting layer (7) provides a good contrast with the protective layer, thereby allowing a high quality TEM analysis.