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Some apps pop up cmd style black windows (in addition to the "main" window with GUI). These command windows are sometimes not very helpful: they just fill up space on the task bar. It would be better to hide them away.

Is there an easy way to remove a certain window completely from screen and from taskbar, but keeping the program running?

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TrayIt! might be what you're looking for. It moves the window to the system tray (notification area).

Another answer here has more details. Confirmed to work on Windows 10; even for multi-window apps.