Ok! So the gnomes are hidden in three backgrounds throughout the game. Clicking them marks them as discovered and a small number hovers over it for a moment.
The first one is located in the storage room to the left. It resembles a small shadow on the shelf.
The second one is located in the forest where Colette runs off to. It's behind a tree to the right in the primary forest background if im not mistaken. I'm a bit hazy on that one but I'm pretty sure that's where it is.
The last one is in the Cerise/Colette bathtub scene when you go to Berry Springs with Colette. Behind a shampoo bottle on the left side of the screen.
These can be clicked throughout multiple save files and still count as long as you save and exit the file after finding it. Once all the gnomes are found, the achievement is granted and a secret area appears on the main menu! Let me know if these instructions are too unclear and I'll try to dig up some screenshots of their locations.