Hiding navigation menu in master page before the javascript message pop up gets called and showing it again after the message pop up

Hello,
This is a first time for me to post here and I searched the solution for this everywhere with no success.
Basically I want to be able to hide the navigation menu object which is declared in the body tag of masterpage before any javascript message pop up gets called. The reason I want to do this is when message box pops up, the navigation menu behind the screen looks very ugly.

So the navigation menu object is defined in the master page, and whenever the page loads it will add about 10~12 items to the menu.
In one of the pages, I use "registerclientstartupscript" to register and call javascript confirm message box
function ConfirmRetrieve() {             var retrieve = confirm('Lock this element for update?');             if (retrieve)          &nb ...