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.