We report on the quasi in situ scanning force microscopy nanotomography which proved to be a key method to effectively obtain a three-dimensional (3D) microdomain structure of a complex ABC triblock morphology. As an example, we studied polybutadiene-block-poly(2-vinyl pyridine)-block-poly(tert-butyl methacrylate) (BVT) thin triblock terpolymer films. We realized a controlled erosion of the material by using low-pressure plasma etching coupled to the scanning force microscope. The 3D reconstruction provides insights into the structural behavior in very thin volume elements revealing morphological details not accessible with other methods.