In this paper, the process effect on the RMS roughness of the $HfO_2$ thin films grown by metal organic molecular beam epitaxy was investigated. The measured RMS roughness is examined to characterize the surface morphology. In order to analyze the factor effects, the significant factors of both the main and the interaction effects were extracted through the effect analysis. In order to compare the regression model with the variable transformation, the effect of each factor and the model efficiency are calculated. The methodology can allow us to analyze the effects between the process parameters related to the process variability.