A scanning electron microscope (SEM) is a complex system, consisting of many sophisticated components. For a systematic characterization, a $2^4$ full factorial experiment was conducted. The SEM components examined include condenser lens 1 and 2 (denoted as A and B, respectively), and Objective lens (coarse and fine-denoted as C and D respectively). A statistical analysis was conduced to investigate factor effects and variations In response surfaces. Among four factors, main effect analysis revealed that A and D were Identified as the dominant factor. Moreover, B showed conflicting effect against C. The $R^2$ of statistical regression model constructed was about 69.6%. The model generated 3D response surface plots facilitated understanding of complex tactor effects.