The charging on unconventional, rough, surface morphologies of polymeric substrates is investigated. The case study is Ar plasma etching of PMMA surfaces with sinusoidal profiles resembling rough profiles. A modeling framework for the description of charging on plasma ''wetted'' two-dimensional (2d) surface morphologies is developed. It consists of models for the calculation of the ion and electron trajectories, the local surface charge density, the potential induced by the surface charge, and a surface etching model. The latter is devised by combining experimental measurements and calculations by TRIM code. Etching rate calculations with and without charging are performed; it is shown that charging affects the etching rate mainly due to the decrease of the ion energy. Calculations are performed for sinusoidal profiles of different amplitude (roughness); as the amplitude increases, the ion energy decreases and the angle of ion incidence increases contributing competitively to the etching rate.