A precise evaluation of the secondary particle production and propagation in the atmosphere is very important for the atmospheric neutrino oscillation studies. The issue is addressed with the extension of a previously developed full 3-Dimensional Monte-Carlo simulation of particle generation and transport in the atmosphere, to compute the flux of secondary protons, muons and neutrinos. Recent balloon borne experiments have performed a set of accurate flux measurements for different particle species at different altitudes in the atmosphere, which can be used to test the calculations for the atmospheric neutrino production, and constrain the underlying hadronic models. The simulation results are reported and compared with the latest flux measurements. It is shown that the level of precision reached by these experiments could be used to constrain the nuclear models used in the simulation. The implication of these results for the atmospheric neutrino flux calculation are discussed.