The magnetic signals from magnetite nanoparticle-labeled PC12 cells were assessed by magnetic force microscopy by deploying a localized external magnetic field to magnetize the nanoparticles and the magnetic tip simultaneously so that the interaction between the tip and PC12 cell-associated Fe3O4 nanoparticles could be detected at lift heights (the distance between the tip and the sample) larger than 100 nm. The use of large lift heights during the raster scanning of the probe eliminates the non-magnetic interference from the complex and rugged cell surface and yet maintains the sufficient sensitivity for magnetic detection. The magnetic signals of the cell-bound nanoparticles were semi-quantified by analyzing cell surface roughness upon three-dimensional reconstruction generated by the phase shift of the cantilever oscillation. The obtained data can be used for the evaluation of the overall cellular magnetization as well as the maximum magnetic forces from magnetic nanoparticle-labeled cells which is crucial for the biomedical application of these nanomaterials.