The effects of substrate Ar-ion milling and Ta adhesion layer on the microstructural and magnetic properties of L1(0)-FePt films prepared on Si, SiO2, and glass substrates were investigated. It was discovered that the relatively large in-plane surface roughness of CrRu/MgO/FePt films deposited on Si substrates was due to the deformation of the CrRu layer when the composition was heated to 550 degrees C. More than an order of magnitude improvement for the in-plane surface roughness was achieved when substrate Ar-ion milling or Ta adhesion layer was incorporated into the process. While the Ta adhesion layer proved to be detrimental to the (200) growth of the CrRu layer, optimal FePt film properties with coercivity values larger than 2 Tesla and out-of-plane roughness less than 1 nm were achieved when only substrate Ar-ion milling was implemented.