I think Cokin sells some sort of clear filter for precisely this sort of thing. Maybe Roscoe has some kind of clear acetate that would work and without introducing optical problems, and shouldn't be too expensive in large sheets.
Another option is to use a matte box or compendium shade with a holder for masks on the front standard. These used to be popular for hokey vignettes and such, but can be used for custom masks cut from black paper or plastic sheet. You can feather the edge of the cut to blend it. If you hunt around on eBay, you can find the Ambico Shade+ fairly cheaply, if you don't want to spring for a Lee system or something fancier, but be sure it comes with adapter rings (or at least one large enough to use with step-up rings on your system), and note that the adapter rings for the Ambico 3x3" filter holder are different from the rings for the Shade+ (which also holds 3x3" filters on the rear standard, as well as masks on the front standard). The Shade+ comes in both a square and rectangular format versions.
" You can feather the edge of the cut to blend it."
How would you suggest to feather the edge? My process is to take the contour marked on the plexi-glass and cut a cardboard mask that will fit in my Cokin holder. Then carefully line up the edge of the mask while looking through the stoped down lens. I then make my two exposures on the same frame. Feathering the edge would make lining up things a little less critical. As it is now the process makes the ultimate hard edge, and allignment has to be bang on.
Any suggestions would be appreciated.
The old vignette masks achieved this feathering just by cutting a jagged, toothed, edge instead of a smooth line, and since the mask is close to the lens and way outside the DOF range, it produced a softer effect. There are scissors available in craft shops that cut various kinds of jagged, deckeled, or toothed edges, so maybe there is one that might work well for this purpose.