Display omitted •Developed molecular model of sliding contact between two non-Gaussian rough surfaces.•Surface topography changes after sliding motion for each plate spacing (δ).•More increase in autocorrelation length signifies more flattening of the surface.•Higher atomic wear and dislocation length are observed for lower plate spacing (δ). Friction plays a significant role in the wear and tear of sliding metallic surfaces, particularly in gears and bearings employed in nano and micro electro-mechanical systems (NEMS/MEMS). To comprehend the nature of dry sliding friction in mechanical devices, it is crucial to investigate surface interactions at the nano-scale. Molecular dynamics (MD) simulation has been utilized in this study to explore how asperities come into contact at this minute scale. Specifically, the interaction between two non-Gaussian rough surfaces is examined at varying dimensionless spacing (δ/Seq), ranging from 3.6 to 2.7. The von Mises strain, atomic wear, and changes in the atomic arrangement after sliding action are obtained for Cu-Cu (soft-to-soft) tribo-pair at a given sliding speed of 10 m/s. The average friction force on the lower surface increased when the space between surfaces was decreased. More percentage changes in surface topography are found for the lesser dimensionless spacing (δ/Seq) of 2.7. The changes in surface topography parameters during sliding action may have an immense effect on the performance of tribo-pair in NEMS/MEMS. A greater increase in autocorrelation length signifies a more pronounced flattening of the lower surface at the lower dimensionless spacing (δ/Seq).