Question: There's an invisible window of some application on my desktop and the only thing detectable about it is its borders as seen in the image below. The window or its edges are not clickable.

[![Desktop with invisible window borders visible](https://i.stack.imgur.com/apYyf.png)](https://i.stack.imgur.com/apYyf.png)

I'm guessing this could be some malware so I need to identify which application is drawing that window. So far, I've gone through the list of running processes in Task Manager to see if something looks suspicious and have scanned the PC with Malwarebytes Anti-Malware to no avail. I also tried using Process Explorer's drag over window tool and it just detects explorer.exe. Could this be a bug in explorer? I'm running Windows 10.

Answer: 
Try using this program from NirSoft: <http://www.nirsoft.net/utils/winlister.html>

You will be amazed at how many windows, both visible and hidden, are actually created by the running software on your computer. That WinLister app will supposedly allow you to identify, and kill, any window.
I guess you could use task manager.

But this seems like its the aero peak thingy.

Try to see if it occurs in safe mode.

Now, since you then commented that it fails to work in safe mode, copy the name of all the processes (MAKE SURE YOUR NOT RUNNING ANYTHING) and put them into a file.

Reboot into safe mode then start opening these processes 1 by 1. You should hit a point where the invisible window pops up. MAKE sure to take notice of each process you start, and cross it off. When this happens, take note of what process started it and open its file location. (RIGHT-click on the process when it is selected then click `open file location`.) Delete that file or find some way to prevent it from startup, and reboot. If all goes well then if won't show up.

NOTE:  

DON'T delete EXPLORER.EXE