When user clicks on a hyperlink, i am opening a popup window which downloads a file. Post download, it shows open/save dialog box. I want to close the popup window once the download is done (when user is prompted for saving the file). I have tried window.close method, but it doesnt work as the context is not the popup window but the open/save dialog box.
I think you can not control it programatically. This is browser-specific thing where some browsers allow you to tick on a check box to close the window and so on.
Browsers have a habit of deciding for themselves whether to try to download a file or open it inside the browser window, depending on the browser used, plug-ins and server settings. It sounds like you might be opening the link in a new window, as if the browser was going to open the file rather than download it, and then the browser has opted for the download. This leaves the user with a downloaded file and a blank window that you have no control over.
To force it to download, you should be able to set the Content-Type header for the target of the link to application/force-download. How you do this will depend on your setup, and whether the file is downloaded directly (in which case it will be a server setting) or via PHP or .Net (in which case it's easy to programmatically set the header). Also make sure that the hyperlink doesn't have a target="_blank"
attribute that opens the link in a new window.