The inner structure of a polystyrene-poly(methyl methacrylate) (PS/PMMA) brush synthesized via two-step surface-initiated radical polymerization was studied by a combination of step-by-step oxygen plasma etching and atomic force microscopy (AFM, "nanotomography" approach). The brush adopts ripple and dimple morphologies upon exposure to toluene and acetone, respectively. The same locations on the brush samples, adopting these two morphologies, were scanned with AFM before and after each etching step. We found that the ripple morphology consists of depressed PS-rich and elevated PMMA-rich elongated domains. In the dimple morphology, the core of the cluster is rich in PS, while the very top layer and the valleys between clusters are rich in PMMA. These experimental observations agree with self-consistent field theoretical predictions of the phase segregated morphologies in nonselective and selective solvents. The 3D structures of the mixed brushes in dry and swollen states were reconstrubted using nanotomography data.