The influence of electrostatic heterogeneity on the electric-field-induced destabilization of thin ionic liquid (IL) films is investigated to control spatial ordering and to reduce the lateral dimension of structures forming on the films. Commonly used perfect dielectric (PD) films are replaced with ionic conductive films to reduce the lateral length scales to a sub-micron level in the EHD pattering process. The 3-D spatiotemporal evolution of a thin IL film interface under homogenous and heterogeneous electric fields is numerically simulated. Finite differences in the spatial directions using an adaptive time step ODE solver are used to solve the 2-D nonlinear thin film equation. The validity of our simulation technique is determined from close agreement between the simulation results of a PD film and the experimental results in the literature. Replacing the flat electrode with the patterned one is found to result in more compact and well-ordered structures particularly when an electrode with square block protrusions is used. This is attributed to better control of the characteristic spatial lengths by applying a heterogeneous electric field by patterned electrodes. The structure size in PD films is reduced by a factor of 4 when they are replaced with IL films, which results in nano-sized features with well-ordered patterns over the domain.