Instead of writing alert you can use jquery ui dialog for stylish dialog box for this add jquery and jquery UI with css.
Code is below:
create a method like this in javascript and
function ShowAlert(message) {
$("#dialog").html(message);
$("#dialog").dialog({
modal: true,
title: "Status"
});
}
In Codebehind :
string message = "Set Message Here";
Page.ClientScript.RegisterStartupScript(this.GetType(), "popup", "ShowAlert('" + message + "');", true);