The whole shot that "went through the computer" has a completely different feel to it than scenes that don't.
Compare 3:38 and 3:44 in https://www.youtube.com/watch?v=bhL8WlDHKaY.
It looks like it was shot with a completely different camera, or going into a mini-dream state.
I mean it's extremely well done. It holds up so well even... jesus christ 30 years later?!
But it's extremely obvious which scenes got the CGI treatement.
Oh, and if this is one of those "once you can see it, you can't unsee it" things: Sorry about that.