A disc drive data storage system is disclosed that includes a disc storage medium having a disc surface. The system also includes an armature and a slider coupled to the armature. The slider supports a transducer head that communicates with the disc storage medium. The slider flies above the disc surface and positions the transducer head proximate the disc surface. Data representing a topography map of the disc surface is stored in a memory. A controller controls the fly height of the slider above the disc surface as a function of the topography map of the disc surface.