This would be the best option. Take the FCS part and make a small box for it to sit in, then use a clear epoxy or polyurethane to encase it.
Otherwise there's two other ways of producing a "different" colour inside a clear part using 3DP.
- SLA: Using a clear material you can "overcure" sections by scanning it with the laser multiple times (or using higher laser powers/different infill param's). I've seen parts with 10 different shades of yellow incased in a clear shell.
- Objet: Using VeroClear as the outer material, and any of the other Objet materials for the bug inside. Only a Connex printer is technically capable of this.
Shapeways doesn't offer either of these processes, but hey, the more you know