As a result of the complexity of special purpose machines many problems arise because of the multiplicity of interacting machine components. Before the assembly of the machine, some of the problems can not be early exposed by virtual simulation and can not be corrected, because one part of simulation chains, i.e. components which are supplied by manufacturers as a black box is not available. To develop these special purpose machines, it is necessary to use hardware in the loop simulation (HiL-simulation). This paper describes principal requirements for software tools used for the HiL-simulation. The experiences of systematic development of the special purpose machine are suggested, which refer to design, functional verification and optimization of an innovative machine concept. Some software tools (Pro/Engineer, SimulationX, Matlab/Simulink/RTW, ETAS-ascet) are discussed and are exemplary used to implement a HiL-simulation strategy for developing free contouring milling machine with high accuracy. A development of a hexapod that is driven with linear telescopic strut consists of subsystems of different engineer disciplines coupling of mechanical and electrical subsystem. The selected software concept permitted further the transfer the coupled simulation on real time hardware. The real time simulation is needed for the hexapod structure of hardware in the loop test rig, which makes possible to test the real CNC controller before the assembly of the machine with sufficient accuracy.