Films of deuterated polystyrene (dPS) and poly(methyl methacrylate) (PMMA) blends, as well as dPS and PMMA and poly(ethylene-co-propylene) (PEP) blends have been spin-cast from toluene solution and annealed at temperatures above their glass transition temperatures for up to 72 hours. Surface topography of the cast and annealed films was measured by atomic force microscopy (AFM). Dynamic secondary ion mass spectrometry (SIMS) was used to study microphase segregation of the polymer films. A series of two-dimensional (2D) images of the films were acquired during sample sputtering. A reconstruction of the sample three-dimensional (3D) structure from 2D data was performed. Spatial distributions of H, D, C, O, and higher mass fragments revealed microphases with dimensions on the order of a few microns. We describe the method that corrects height distortion to 3D SIMS images. After sputtering, AFM is used to produce a topographic image of the area analyzed by SIMS. The surface height variation array from SIMS data was compared with that observed by AFM. A limitation of the correction method is discussed.