This paper describes the application of SRNA Monte Carlo package for proton transport simulations in complex geometry and different material composition. SRNA package was developed for 3D dose distribution calculation in proton therapy and dosimetry and it was based on the theory of multiple scattering. The compound nuclei decay was simulated by our own and the Russian MSDM models using ICRU 63 data. The developed package consists of two codes SRNA-2KG, which simulates proton transport in the combinatorial geometry and SRNA-VOX, which uses the voxelized geometry using the CT data and conversion of the Hounsfield’s data to tissue elemental composition. Transition probabilities for both codes are prepared by the SRNADAT code. The simulation of proton beam characterization by Multi-Layer Faraday Cup, spatial distribution of positron emitters obtained by SRNA-2KG code, and intercomparison of computational codes in radiation dosimetry, indicate the immediate application of the Monte Carlo techniques in clinical practice. In this paper, we briefly present the physical model implemented in SRNA pack age, the ISTAR proton dose planning software, as well as the results of the numerical experiments with proton beams to obtain 3D dose distribution in the eye and breast tumor.