*Is* there such a tool? From what (little) research I've done, I wouldn't think so.
See, the Playstation doesn't have static layers like older consoles that can be toggled on and off. Instead, it apparently displays everything (except for a rather basic sprite mode) as 3D textures which, in the case of a 2D game, are simply rendered with no perspective so they appear "flat".
Whatever layers you can see (like a half-dozen distinct backgrounds, a sprite layer, a boss layer and a few transparencies while we're at it, why not?) are defined and handled by the game's engine. No emulator would be able to separate these layers since it would all be a bunch of separate tiles and textures to it. Your best bet would be to find a tool specifically designed to extract the layers of a given game or games using the same engine.
From what I remember from Zeric (Mega Man 8 ) and Revned (Castlevania: Symphony of the Night), they mapped their respective games by taking a lot of screenshots and removing the backgrounds using whatever methods worked best (color replacement for example), and using a tool like GLIntercept to capture all the individual tiles/textures loaded in memory in OpenGL I believe (it's been several years).
Unfortunately, mapping most modern 2D games runs into the same problems of having to separate layers by hand and thus taking a lot more time than desired, in addition to the risk of more imperfections cropping up (like removing too many pixels by accident, or completing partially visible tiles with similar yet wrong ones). The only real way around that is to be a master coder who can decipher a game's graphics and levels format and extract them directly, and that's easier said than done.
