We present a numerical scheme to simulate a moving rigid body with arbitrary shape suspended in a rarefied gas micro flows, in view of applications to complex computations of moving structures in micro or vacuum systems. The rarefied gas is simulated by solving the Boltzmann equation using a DSMC particle method. The motion of the rigid body is governed by the Newton-Euler equations, where the force and the torque on the rigid body is computed from the momentum transfer of the gas molecules colliding with the body. The resulting motion of the rigid body affects in turn again the gas flow in the surroundings. This means that a two-way coupling has been modeled. We validate the scheme by performing various numerical experiments in 1-, 2- and 3-dimensional computational domains. We have presented 1-dimensional actuator problem, 2-dimensional cavity driven flow problem, Brownian diffusion of a spherical particle both with translational and rotational motions, and finally thermophoresis on a spherical particles. We compare the numerical results obtained from the numerical simulations with the existing theories in each test examples.