FAB 3000 will export anything displayed on the screen to 3D STEP.
Do you wish to have the holes (filled). If yes, convert the drill layer to gerber (i.e round) and then export that layer as a STEP. Here's a sample tutorial movie:
Note: If you wish to have a "hollow" cylinder (in the STEP), you can convert the Round pads to Donut pads; and then export to STEP.
Thanks again, and I look forward to hearing from you.