Gone Girl
David Fincher's Gone Girl is an excellent example of a film with invisible special effects. Although Gone Girl may not seem like a film that utilizes a significant amount of VFX, it's only because Fincher's use of CGI is imperceptible to the untrained eye.
The McMansion rented by Nick and Amy Dunne is lit so perfectly that it hardly looks as though it's shot on a sound stage. However, an effects breakdown reel shows that everything beyond the house's walls was a green screen. Building the house on a sound stage allowed Fincher the flexibility to shoot without concerns of natural lighting or framing.