Methods are described for etching metal layers that are difficult to volatize, such as cobalt, nickel, and platinum to form an etched metal layer with reduced surface roughness. The methods include pretreating the metal layer with a local plasma formed from a hydrogen-containing precursor. The pretreated metal layer is then reacted with a halogen-containing precursor to form a halogenated metal layer having a halogenated etch product. A carbon-and-nitrogen-containing precursor reacts with the halogenated etch product to form a volatile etch product that can be removed in the gas phase from the etched surface of the metal layer. The surface roughness may be reduced by performing one or more plasma treatments on the etching metal layer after a plurality of etching sequences. Surface roughness is also reduced by controlling the temperature and length of time the metal layer is reacting with the etchant precursors.