The interaction of plasma with polymeric substrates generates both roughness and charging on the surface of the substrates. This work, toward the comprehension and, finally, the control of plasma-induced surface roughness, delves into the intertwined effects of surface charging, ion reflection, and secondary electron-electron emission (SEEE) on roughness evolution during plasma etching of polymeric substrates. For this purpose, a modeling framework consisting of a surface charging module, a surface etching model, and a profile evolution module is utilized. The case study is etching of a poly(methyl methacrylate) (PMMA) substrate by argon plasma. Starting from an initial surface profile with microscale roughness, the results show that the surface charging contributes to a faster elimination of the roughness compared to the case without charging, especially when ion reflection is taken into account. Ion reflection sustains roughness; without ion reflection, roughness is eliminated. Either with or without ion reflection, the effect of SEEE on the evolution of the rms roughness over etching time is marginal. The mutual interaction of the roughness and the charging potential is revealed through the correlation of the charging potential with a parameter combining rms roughness and skewness of the surface profile. A practical implication of the current study is that the elimination or the reduction of surface charging will result in greater surface roughness of polymeric, and generally dielectric, substrates.