In this study, atomic force microscopy (AFM) is used to investigate the heterogeneity of blenlded films of poly(methyl methacrylate) (PMMA) and polybutadiene (PB) on silicon substrates before and after annealing. The blended films with different ratios of PMMA to PB are prepared by spin casting onto silicon substrates from solution. The surface morphology and composition of these cast films are investigated using tapping mode and force mode AFM. Annealing the samples in air at 75 +/- 5 degreesC causes changes in the relative chemical and mechanical differences between PMMA and PB, so the phase image contrast is studied as a function of annealing time. The effect of tapping force level on phase image contrast is also explored. To identify the different components in polymer blends and to understand the influence of relative surface stiffness on the phase images, nanoscale indentation measurements are made on the observed phase-separated regions. Interpretation of AFM results is aided by data collected from both conditioned and annealed PB and PMMA films using Fourier transform infrared spectroscopy, dynamic mechanical analysis, differential scanning calorimetry, and contact angle measurements. A loss in phase contrast between PB-rich and PMMA-rich regions is observed as a function of heating time. This observation correlates well with the increases in glass transition temperature, modulus, and polarity of pure PB with respect to pure PMMA.