What it sounds like you want to do is hide an app's window. The "window" is something most apps need to interact with so again the answer is you can't close it.
Try Outtasight found with https://www.google.com/webhp?sourceid=chrome-instant&ion=1&espv=2&ie=UTF-8#q=hide%20window%20of%20open%20app
I was looking through the settings of the Slack desktop app and found that there were limited settings for startup. I am not very active with this app and therefore don't need it to open a window on startup, but I do want it to run in the background so I can get notifications from the application. (I tried their forum and I don't suspect they will do anything about it.) I was wondering if there is some way (with maybe Task Scheduler or some third party app) to close a window on startup without actually ending the task that is running the program. The only thing I have found is a way to stop a task, which would not allow me to receive notifications.
Windows 7, 64 Bit