Anyway to open a pop-up in its own browser instance

[CW]

I notice that I pop windows from the same parent window, the child windows
and parent window are related by the same browser instance. If I am working
on any of these windows and another child window (or the opener window)
calls window.focus, that window will pop on top. This is not a desired
behaviour in a chat program I am working on. Is there anyway to ensure that
new pop-up window is not in anyway related to the parent?

Thanks