In this article, theoretical modelling of electromagnetic field distribution in the exposed thin film during lithographic process of microlenses array formation is presented. While studying topography of microlenses by means of atomic force microscopy we have found that various diffraction effects are observed due to the small dimensions of microlens patterns comparing to the wavelength. In this article we use finite-difference in time domain (FDTD) method to model electromagnetic field distribution in complex pattern-film geometry. Within FDTD, we solve Maxwell equations numerically, which enables us to model any type of geometry or material properties. Therefore, the effects of different perturbations, like pattern boundary imperfections or thin film roughness can be studied within this method, showing their effect on the electromagnetic field distribution within illuminated chalcogenide thin film.