[en] A high energy accelerator design performance is achievable only with a dedicated beam cleaning system embedded in the lattice. The system has to protect the superconducting magnets against quench, to decrease accelerator related backgrounds in the detectors and to protect accelerator components, environment and personnel from irradiation. Different collimation schemes are designed to meet a specific requirements of different accelerators. Even in good operational conditions, a finite fraction of the beam will leave the stable central area of accelerator because of beam-gas interactions everywhere along the accelerator ring, intra-beam scattering, proton-antiproton collisions in the IPs, RF noise, ground motion and resonances excited by the accelerator magnet nonlinearities. These particles produce a beam halo which is traveling simultaneously with main beam, but outside the beam core. As a result of beam halo interactions with limiting aperture, hadronic and electromagnetic showers are induced in accelerator causing accelerator components heating, irradiation and accelerator related background in the detectors. A beam collimation system is used for the beam halo interception in a specially equipped warm part of accelerator. Collimation system design based on a realistic Monte-Carlo simulations using a system of computer codes is described: A multi-turn particle tracking through the accelerator and beam halo interactions with the collimators are done with STRUCT code. All lattice components with their real strengths and aperture restrictions are taken into account during these calculations. Particles lost in the accelerator are stored in the files for the next step of calculations using MARS code. Particle loss induced hadronic and electromagnetic showers, secondary particle transport in the accelerator and detector components, including shielding with real materials and magnetic fields are done with MARS code. ANSYS is used for collimation system elements thermal and stress analyses. The codes application at collimation system design for the TEVATRON and 3 GeV ring of the Japan Hadron Facility (JHF) is shown. (author)