Atomic force microscopy based power spectrum density (PSD) method along with conventional methods such as line, grain height, root mean square (rms) roughness, is used to probe complex Hg–Au interactions i.e. the amalgamation of smooth gold nanostructures (Au–ns) and partial dissolution of irregular edges of interconnecting Au–ns networks due to Hg. We have demonstrated for the first time the use of the PSD method to gain significant insights into the directional anisotropy of resultant Hg–Au–ns and the range of Au–ns responsible.