Yup, you can do eye replacement in Shake (indeed if you’ve seen eye replacements done in high end films between the late nineties and last year there is a high likelihood they were comped in Shake).
Shake and after effects aren’t true 3d compositors (the likes of Nuke and Fusion are). In Shake you use the Multiplane node (look it up in the manual for more info as there’s quite a section devoted to it).
I’d consider shake and after effects to be more like 2.5d (in the fact they can’t import 3d models, use primitive shapes to project image data onto, or use materials/lighting or truly distort in 3 dimensions, as you can in a true 3d app). They allow you to place image planes in 3d space and animate a camera (i.e. imagine setting up flat cards in the real world at varying distances from you and then moving a camera through the cards). This may seem limiting but it is actually pretty useful for matte paintings and crowd replication (especially coupled with camera data out of a 3d matchmove application).
After effects’ implimentation of a 3d-esque environment is better and less buggy than Shakes multiplane.
Goodluck!
andrew