We perform numerical simulations of a three-dimensional (3D) time evolution of pure gravitational waves. We use a conformally hat and K = 0 initial condition for the evolution of the spacetime. We adopt several slicing conditions to check whether a long time integration is possible in those conditions. For the case in which the amplitude of the gravitational waves is low, a long time integration is possible by using the harmonic slice and the maximal slice, while in the geodesic slice (alpha = 1) it is not possible. As in the axisymmetric case and also in the 3D case, gravitational waves with a sufficiently high amplitude collapse by their self-gravity and their final fates seem to be as black holes. In this case, the singularity avoidance property of the harmonic slice seems weak, so that, it may be inappropriate for the formation problems of the black hole. By means of the gauge-invariant wave extraction technique we compute the waveform of the gravitational waves at an outer region. We find that the nonlinearity of Einstein gravity induces the higher multipole modes even if only a quadrupole mode exists initially.