The embodiments of mechanisms described enables improved planarity of substrates, which is crucial for patterning and device yield improvement. Chemical-mechanical polishing (CMP) is used to remove film to planarize the substrate before the final thickness is reached or before all removal film is polished. The substrate is then measured for its topography and film thickness. The topography and thickness data are used by the gas cluster ion beam (GCIB) etch tool to determine how much film to remove on a particular location. GCIB etch enables removal of final layer to meet the requirements of substrate uniformity and thickness target. The mechanisms enable improved planarity to meet the requirement of advanced processing technologies.