How would I draw something on the screen ? not the console window but the entire screen, preferably with the console minimised.

Also, would it show up on a printscreen ? It better not :P
What I want to do is create something like a layer on top of the screen that only me and my aplication are aware of yet still be able to use aplications as usual.

I thought the drawing part would have been done thousands of times by now but google has failed in returning any promising results.

Are you talking about making a window for your program to run in? If so, look into Win32 and Direct3D (for Windows applications). Note that, if this is indeed what you're trying to do, "drawing" to a window with Direct3D is not all that simple.

You could also look into some 2D libraries like SDL that make the process a lot easier.

Maybe I should give an example.
Let's say I want 2 yellow squares 5 by 5 pixels in size appearing in the center of the screen on top of all the other applications, unclickable and invisible in a printscreen.

How can I do that ?