In this study we report investigation of the polymer film morphology modifications during their corona poling for fabrication of nonlinear optically (NLO) active materials. We demonstrate that at certain poling conditions surface and spatial inhomogeneities in the poled area of the sample appear. Densities of the inhomogeinities depend on the strength of the poling field, the sample temperature during the poling, and the prepoling conditions. Optimization of the poling conditions directed toward avoiding surface modifications enables us to increase the overall observable effective nonlinearity of the sample up to 10 times. To investigate, understand, and eventually explain the formation of the spatial and surface structure inhomogeinites in the poled material we have used optical, second harmonic, and scanning electron microscope measurements, as well as the conductivity measurements of the thin films. We present results of poled polymer host guest films where (dimethylamino)benzylidene-1,3-indandione and low dipole moment 2,2',2 ''-(4,4',4 ''-nitrilotribenzylidene)triindan-1,3-dione were used as guests in poly(methyl methacrylate), polystyrol, and polysulfone matrixes doped at 10 wt %.