In this paper, we demonstrate the applicability of focused ion beam (FIB) preparation followed by tapping mode atomic force microscopy (TMAFM) to analyze model interphase thicknesses in high density polyethylene/polystyrene/poly(methyl methacrylate) (HDPE/PS/PMMA) ternary polymer blends prepared by melt mixing. Previous work has shown that, in a polyethylene matrix, this blend exhibits a dispersed phase composed of a well-segregated PMMA core and a PS shell. Control of the PS/PMMA composition ratio allows for the control of shell thickness and hence this blend provides an excellent model system to analyze interphase thicknesses. A focused ion beam preparation was applied to the melt blended samples to prepare very smooth surfaces without mechanical deformation (i.e., no plowing or interfacial debonding), while TMAFM was used to obtain high-resolution images of the composite droplets in order to measure the mean diameter of the droplets and PS shell thickness. It is shown that the three polymer components have different ion beam etching rates, which results in a topological contrast between the phases of the blends when viewed by tapping mode atomic force microscopy. In this case, PMMA has the highest etching rate, while PS has the lowest and HDPE is intermediate. This high level of contrast between the phases allows for a clear identification of the PS interphase. Even the fine features of particles in the process of coalescing can be clearly identified. To ensure that this procedure was not altering the blend phase sizes in any way, average composite droplet diameters obtained with FIB preparation and TMAFM measurements were compared with the classic technique of cryomicrotome preparation and SEM measurements. The dispersed phase size data from the two procedures compare well. The FIB/TMAFM approach allows for the estimation of the PS interphase thicknesses from 100 to 200 nm depending on the PS/PMMA composition ratio. The approach presented here avoids the pitfalls associated with microtomy such as microvoiding, deformation of the materials and debonding at the interphase. It also eliminates the need for extraction of polymers with selective solvents and staining techniques used to provide contrast. This technique provides significant advantages for the analysis of multicomponent polymer blends or blends with complex morphologies. It also provides a first step toward a new approach for analyzing interphase thickness in polymer blends.