The atomic force microscope (AFM), a three-dimensional imaging tool that can measure structures from the atomic level to micron scale, has been combined with an inverted optical microscope capable of confocal imaging. The robust design of this microscope, termed the BioScope, enables the operator to use fluorescent markers on a wide variety of biological specimens to determine internal structure to 200 nm resolution and determine surface morphology of the same sample to 20 nm resolution while imaging under physiological conditions. In this report we demonstrate the capabilities of the BioScope by examining living Xenopus retinal glial (XR1) cells, Drosophila polytene chromosomes and colloidal gold-labeled plasmid DNA.