I believe you are working with the RadWindow for ASP.NET AJAX. If this is the case I advise that you examine the following KB article that treats showing it above a heavy weight objects like pdfs and sliverlight: http://www.telerik.com/support/kb/aspnet-ajax/window/control-is-shown-behind-a-heavy-weight-object-pdf-flash-activex-etc.aspx
The essence is that you need to set the Overlay property to true so that an additional iframe element is created behind the control so it can stay above the heavy object. The RadWIndow's content is already an iframe that hosts the page you have pointed it to, so this is why it stays on top.
All the best,
the Telerik team
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