Unlike in a windows forms app, a web application doesn't have a "parent" or "child" window concept. At least not from the perspective of the server. You have to deal with this relationship from the client-side perspective.
A window opened with javascript should have the "window.opener" property which will refer to the browser window that opened it. But remember, this is only on the client side of things. Using "window.opener" you could then reference a control in the opener window (parent) and assign it a value.
Master pages has no affect on this behavior.
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Peter