My scenario I have is I have a physical PCB and no CAD/Gerber files available for it. I will need to somehow get all the pads in to FAB3000 to allow me to cut out a stencil for it. Is it possible to scan the PCB into a pdf or image file and import it to FAB3000 to be able to get the pad oultines? Or is there another method of doing so?
Yes, you can import a scan. PDF's are not the best choice. JPG's or BMP's will work better.
Another method would be to import your scanned image as a background image in FAB 3000. See "Set Background Image" under the setup menu.
The FAB 3000 help guide has an overview of both setting the background image (search for set background image) and importing bitmap files. (search for File > Import > Image)