I'm trying to write a semi transparent click trough program to use like onion skin over my 3d application.
the one thing I couldn't find googling is how to make the window click trough. is there an attribute or something for it in tkinter? or maybe some way around it?
You can use PyAutoGUI and Tkinter to:

Get current mouse position relative to desktop coordinates.
Minimize tkinter window or drag it out of the screen.
Simulate click event when the window will be hidden.
Return back tkinter window.

It should work but I'm not sure how fast would it be.
python 3.4 tkinter, click trough window