Doesn't sound like best of the approach (I mean you could show pop-up client side)... However, if you want to accomplish this...
You have have a hidden asp:Button on your aspx and attach a event handler to it and write the code that you want to have executed upon clicking Yes on the confirm button.
And modify your RegisterStartupScript as below
type= ClientScript.RegisterStartupScript(typeof(Page), "exampleScript", "if(confirm('are you confirm?')) { document.getElementById('btn').click(); } ", true);