Two different sputtering modes, co-sputtering and multilayer-sputtering, were used to fabricate FePt:Ag granular thin films. It is observed by the MFM and TEM images that smaller magnetic domain patterns and grains are more uniformly distributed in the co-sputtered granular films compared to in multilayer-sputtered ones. This difference in the microstructure is explained to be attributed to the more randomly distributed Ag atoms in the co-sputtered films. Further study on in-depth defects in these films confirms this explanation.