Let's clarify: do you want this tool to run on client side or on server side?
If you want on client side, than you got your answer from OriginalGriff: you can't in general (first of all not how you intended to do it). Well, you could under special circumstances, but let's not dig into this until you have clarified (for example using Silverlight full trust:
http://silverlightedweb.blogspot.hu/2011/12/how-to-get-unrestricted-access-in.html[
^]).
If you want this tool to run on server side, than what you have seen that "
in task manager its showing that is its running in background" is exactly what it should happen. IIS is a service running under special user account - even if you specify application pool account and you impersonate that account the you will have different session. So your application won't have a GUI visible to anyone :(. This way you should run only executables that have command line interface and no user interaction is needed.