A numerical model for assessment of the effective dose and ambient dose equivalent produced by secondary cosmic ray particles of galactic and solar origin at commercial aircraft altitudes is presented. The model represents a full chain analysis based on ground-based measurements of cosmic rays, from particle spectral and angular characteristics to dose estimation. The model is based on newly numerically computed yield functions and realistic propagation of cosmic ray in the Earth magnetosphere. The yield functions are computed using a straightforward full Monte Carlo simulation of the atmospheric cascade induced by primary protons and a-particles and subsequent conversion of secondary particle fluence (neutrons, protons, gammas, electrons, positrons, muons and charged pions) to effective dose or the ambient dose equivalent. The ambient dose equivalent is compared with reference data at various conditions such as rigidity cut-off and level of solar activity. The method is applied for computation of the effective dose rate at flight altitude during the ground level enhancement of 13 December 2006. The solar proton spectra are derived using neutron monitor data. The computation of the effective dose rate during the event explicitly considers the derived anisotropy i.e. the pitch angle distribution as well as the propagation of the solar protons in the magnetosphere of the Earth.