Upon returning to the US John went to work for Industrial Light & Magic where he animated several key scenes in Terminator 2: Judgment Day (1991), most notably where the shotgunned head of the chrome terminator re-seals itself.

John VFX supervised Stay Tuned (1992) for Rhythm & Hues Studios, and In the Line of Fire (1993), My Life (1993), The Pelican Brief (1993), Wolf (1994), Johnny Mnemonic (1995), Judge Dredd (1995), The Cable Guy (1996) and City of Angels (1998) for Sony Pictures Imageworks.

In 1998 Mr. Nelson left Sony to Senior VFX supervise Gladiator (2000) for which he won the Academy Award for Best Visual Effects (2001). After K-19: The Widowmaker (2002) and the Centropolis sections of The Matrix Reloaded (2003) and The Matrix Revolutions (2003), Mr. Nelson supervised all the VFX in I, Robot (2004) and Iron Man (2008) both of which were nominated for the Academy Award in Visual Effects. John is a member of the Academy of Motion Picture Arts and Sciences, the Visual Effects Society, the the International Cinematographers Guild and the Director's Guild of America.