Fangoria has posted an interview they did with Gillian on the set of Hannibal just last month.
“The X-Files started shortly after Silence of the Lambs came out, and Chris Carter told me shortly after we began that Scully was in fact based on the character of Clarice Starling. And although this character is different, something about it feels like we’re on the same conversations, you know. It has come full circle. The relationship here is somewhat elusive. My character knows its serving a purpose, being with Hannibal and I think she feels protective over him. We learn that she is retired but he wouldn’t accept that, so now he is her only patient. They feed off each other, if you will.”
You can read the full interview on the Fangoria website here.