The methodology making available an analysis of high frequency (HF) wave propagation in ionosphere with the presence of sporadic E layer (Es) is presented. A numerical ray tracing code is exploited to estimate the ray-paths through ionosphere comprising E, Es, F1 and F2 layers. A number of vertical and oblique sounding ionograms were emulated in the frame of NIM-RT propagation model. Fairly good resemblance between measured and simulated ionograms with the presence of Es layer was achieved. Numerical modelling provides an assessment of a number of parameters defining Es layer features including virtual height of the layer and its transparency.