Scanning tunneling microscopy (STM) and transmission electron microscopy (TEM) were used to quantify and characterize CoSi2surface roughness and CoSi2/Si interface roughness. Roughness at the CoSi2/Si interface has been reported to be on the order of 20 nm, enough for concern in shallow junction formation in submicron complementary metal–oxide semiconductor devices. Interface roughness is tied to surface roughness by thermal grooving kinetics and by thermodynamics. Hence, a correlation should be seen between roughness at the interface and the surface, yielding information regarding grooving kinetics. This study focused on the processing time dependence of surface and interface roughness. This roughness was quantified using the average roughness measurement technique. The roughness values obtained by TEM were compared to those obtained by STM. Both were fitted to thermal grooving kinetics equations.