Function: The MFP-3D integrates optical microscopy and atomic force microscopy (AFM). Sample features are located using brightfield, phase contrast, or fluorescence, then probed at the nanometer scale with an AFM scan. AFM is combined with such powerful optical microscopy techniques as confocal microscopy, including the capability to synchronize with confocal measurements. The superluminescent diode and additional optics minimize interference with fluorescent signals. Advanced software capabilities allow the researcher to display results intuitively in 3D, then use powerful analysis and scripting tools to extract and graph quantitative information.