Scanning resonator microscopy (SRM) is developed to integrate whispering gallery mode (WGM) sensing with atomic force microscopy (AFM). The hybrid technique combines the exquisite refractive index sensing of whispering gallery mode resonators with the topography mapping capabilities of AFM. A 45 μm diameter barium titanate microsphere is attached to the end of a conventional AFM cantilever and acts as both a WGM resonator and stylus for mapping surface topography. Calibration plots, taken in contact-mode feedback, show that the WGM spectrum responds to changes in both solution and substrate refractive index. SRM imaging of a glass substrate reveals changes in surface refractive index that correspond to a small, 36 nm high feature measured simultaneously in the contact-mode topography image. Spectral measurements confirm that the contrast arises from refractive index changes and not coupling with sample topography, thus validating the approach. Additional measurements on thin polymer films and protein-coated surfaces are presented and discussed in terms of possible areas of application for SRM.