Is there any way I can get hold of the scanners dialog handle so I can force it to be top most? Alternatively is there another way I can achieve this through the SDK?
Basically I'm opening it from a system tray icon so there isn't a main window which is why I assume its going to the back of open windows.
TWAIN specification does not have functionality that allows to get handle of the scanner's UI dialog. For solving your task you need analyze opened windows.