There is no special routine for clipping points, but the GRToolbox can be used for it combining three roll commands:
gr_roll -f test.dat -i 0 1 -c| gr_roll -i 2 3 -c| gr_roll -i 4 5
The reult will be all the points that lie within the X-interval 0 to 1 and the Y-interval 2 to 3 and the Z intervall 4 to 5.