The study of internal mechanics of single cells is paramount to understand mechanisms of mechanoregulation. External loading and cell-mediated force generation result in changes in cell shape, rheology, and the deformation of subcellular structures such as the nucleus. Moreover, alterations in the processes that regulate these responses have been further correlated to specific pathologies. Cellular deformation is often studied through application of forces in the environment of the cell, relying on strain and stress transfer through focal adhesions and the cytoskeletal system. However, the transfer of these external forces to internal mechanics can introduce uncertainties in the interpretation of subcellular responses. Our group has focused on minimally-invasive techniques for the study of internal mechanical perturbation and mechanobiology measures. We have been particularly interested in multimodal imaging methods that combine and leverage nanoscale spatial localization, visualization, biophysical and physico-chemical analysis features to reveal information that cannot be attained by any single method alone. We recently fabricated novel atomic force microscopy (AFM) cantilevers, functionalized to generate small, highly-localized magnetic fields, for the controlled force application and sensing of single cells. In combination with AFM and fluorescence microscopy detection capabilities, this technique enables the selective stimulation and monitoring of cells injected with superparamagnetic microbeads. Though the targeted magnetic force application, we are able to apply various waveforms to direct the microdisplacements of the injected beads to allow insight into the structural architecture of the cell. Coupling this with AFM techniques further yields insight into internal and external mechanics over time. This technique can be extended to include studies of intranuclear strain dynamics through fluorescent labeling of specific cellular targets and image post-processing algorithms such as hyperelastic warping. Furthermore, the ability to alter the culture environment (e.g. to manipulate osmotic pressure or enable drug delivery) allows this technique to be a powerful single cell analysis tool for a diverse set of applications. We demonstrate the feasibility of this technique through the localized application of low magnetic fields that produce bead displacements in the micrometer scale. The effects of larger induced magnetic fields in the displacement field are also presented, along with validation and viability studies, and a range of practical applications for the study of single cells.