Fe-doped SrRuO3 thin films were grown on SrTiO3 (STO) substrates by using the Pulse Laser Deposition (PLD) method. Fe concentrations in the SrRuO3 thin films ranged from 0 % to 11 % to manifest the effect of Fe doping on their microstructure. Lattice constants of the films did not show obvious changes with the Fe doping whereas surface morphologies drastically changed from stepped to island structure with increasing Fe. X-ray reflectivity revealed that the surface and interfacial roughness decreased with increasing concentration of Fe. Surface roughness of the films was confirmed by atomic force microscopy. Therefore, a precise determination of film roughness as well as its growth mechanism using X-ray and AFM is exploited to correlate the Fe doping with structural disorder.