I don't know how it's done with that particular software, but the fiducials I always use are just a small dot of copper with the solder mask and silk screen cleared in its immediate vicinity. This must be possible with any competent software.
I use Eagle, and there it's just a filled circle in the top copper layer, with a larger filled circle of solder mask at the same coordinate. In Eagle, drawing in the solder mask layer (tStop) removes the solder mask. I then place these in convenient places at rounded coordinates as pretty much the last step in designing the board. I therefore manually ensure there is no silkscreen within the solder mask hole.
I just checked, and my standard fiducial is a 20 mil diameter copper dot within a 50 mil diameter solder mask hole. I have had several different manufacturers make boards with these fiducials on them, and never received any complaints. You need to have at least two in opposite corners. For large boards I usually put one in each corner.