Fluorescence microscopy, in combination with atomic force microscopy (AFM), reveals that rhodamine-labeled lysozyme adsorbs strongly from aqueous solution to polishing marks of nanometer depths on fused silica surfaces. The fluorescence and topographical images correspond closely. Fluorescence intensity varies by as much as a-fold over the same region where the topography varies over 2.5 nm. Desorption of lysozyme from the surface occurs on rinsing with solutions of increased ionic strength or decreased pH, showing that reducing the Coulombic attraction enhances desorption. Different polishing marks behave differently with respect to desorption: the fluorescence pattern on the surface changes when the ionic strength of the rinsing solution reaches 0.1 M, indicating that some polishing marks are more strongly adsorptive than are others. The desorption depends on pH, which is consistent with the known variation in the charge of silica surface. A superpolished silica photomask, which has significantly fewer polishing marks on the nanometer scale, has significantly less adsorption of lysozyme, suggesting that the topography on the nanometer scale influences adsorption.