In AFNI itself, you can click the "Pos" button under the colorscale in "Define Overlay". This will show only positive Overlay functional values -- so if you set the overlay brick to be the t-statistic, that's what you'll get.
In 3dcalc, you could use an expression like 'a*step(a-3)' to select out voxels that have values greater than 3.
You could do this combined with clustering as well, in 3dmerge, if you chose the correct combination of "-1" editing operations.