A method for analyzing a sample with a charged particle beam including directing the beam toward the sample surface; milling the surface to expose a second surface in the sample in which the end of the second surface distal to ion source is milled to a greater depth relative to a reference depth than the end of the first surface proximal to ion source; directing the charged particle beam toward the second surface to form one or more images of the second surface; forming images of the cross sections of the multiple adjacent features of interest by detecting the interaction of the electron beam with the second surface; assembling the images of the cross section into a three-dimensional model of one or more of the features of interest. A method for forming an improved fiducial and determining the depth of an exposed feature in a nanoscale three-dimensional structure is presented.