Magnetotactic bacteria and live human platelets were investigated by atomic force microscopy (AFM). Contributions to the measured height profiles due to different local mechanical properties were determined by force modulation microscopy. We found that in the case of the thick-walled bacteria the intracellular structures did not significantly influence the overall topology measured by AFM. The magnetosomes were only visible in the force modulation mode, in the case of the platelets the images were dominated by the cytoskeleton and the organelles. The local composition of the cytoskeleton was analyzed by subsequent steps of degradation of certain fibers with specific drugs during AFM imaging.