Step 3: Prepare the Print for molding
To smooth the surface to the level that I wanted, I quickly realized that sanding the surface of the print wasn't going to work - the surface was too hard and inconsistent - so I had to come up with something else. The technique I settled on was one where I'd flood the surface with 2-3 coats of laquer sanding sealer (light sanding between coats) followed by rattle-can FILLER primer (not sealer) and a series of passes of sanding, chasing details, priming, sanding, chasing details, etc, until I was happy with the surface. Dupli-Color brand Filler-Primer seems to work the best for me - most other brands I tried stay too gummy. Epoxy-based filler primer would be ideal - great build up and super-easy sanding characteristics - but it's a bit expensive ($20/can).
Once your surfaces are smooth, it's time to fill in undercuts and open loops that might "trap" the mold as well as just make parts harder to extract from the molds. You don't have to make the areas "flush" but it's a good idea to minimize them without compromising the design. You'll also want to add small details and details that didn't come through in the print. For example, areas where a bump map is used on your model, you'll have to recreate that detail with clay (epoxy sculpt in my case) or hard wax. This is also the stage where you can cover one part of a mating surface with clay and press it onto it's corresponding part on the model to create a "key" so that when the model is assembled it will fit together perfectly.
Model preparation is important - remember that the surface quality of your castings will never be better than that of the "master" object - so take your time in the preparation steps.