In this thesis, we present the design and applications of a cryogenic atomic force microscope (AFM) for characterization of nanostructures. The cryogenic AFM with a conductive tip can measure DC current through nanostructures. We use quartz tuning fork (QTF) as the force sensor. Unique coarse z motor design provides reliable autoapporach in the Z direction. AFM imaging with 10nm horizontal and ~2 angstrom vertical resolution has been achieved. We have used this AFM in the current-voltage characterization of diodes, and, with a modified sensing mechanism, electrical force microscopy (EFM) and magnetic force microscopy (MFM) have been demonstrated.