Thavitinaidu,Thanks for your help. I had the same requirement and I could fix it with your suggestion.I am putting my findings here if anyone is interested.The GUIDs of all dockable windows can be found in the registry at the following location.HKEY_CURRENT_USER\Software\ESRI\Desktop10.2\ArcMap\DockingPaneLayouts\panestate\Pane...And the code to remove the dockable window is as below.
IDockableWindowManager docWinMgr = pApps as IDockableWindowManager;
UIDClass pUID = new UIDClass();
pUID.Value = GUIDValue;
IDockableWindow pDocWindow = docWinMgr.GetDockableWindow(pUID);
if (pDocWindow != null)
{
pDocWindow.Show(false);
}
Thanks,S.