Same way that your are doing using JavaScript.
But Register that function from codbehind using
ClientScript.RegisterStartupScript(this.GetType(), "Confirm",
"<script>Confirm('" + Are You Sure ?+ "');</script>");
or if use ajax in your page then ScriptManager instate of ClientScript
aur else you can use this code also
<asp:button runat="server" id="Button1" onclick="Button1_Click" style="display:none;" />
...
<script type="text/javascript">
function callBack(args)
{
document.getElementById("Button1").click();
}
function openConfirm()
{
radconfirm("Are you sure?", callBack);
}
</script>