It's simple to translate MouseX,MouseY to whatever your 3D scale is.
If you don't want do translate, one idea is to draw your 3D scene in a 1:1 pixel scale, meaning that if your window is 800px wide, create your scene as 800 units wide. Because the mouse still exists in two dimensions (MouseX,MouseY) there's no issue in translating that to "3D X,Y". That's how i've seen 2D-in-3D systems work.
If you don't want do translate, one idea is to draw your 3D scene in a 1:1 pixel scale, meaning that if your window is 800px wide, create your scene as 800 units wide. Because the mouse still exists in two dimensions (MouseX,MouseY) there's no issue in translating that to "3D X,Y". That's how i've seen 2D-in-3D systems work.