How to make modal popup like gmail (when we try to upload exe the pop up that generates covers scrollbar of the page)
GMail runs on a iframe and the overlay div is not inside this iframe, so it stays on top o the iframe consequently on top of the scrollbar.
Code from GMail
html, body {
    height:100%;
    margin:0;
    overflow:hidden; /* no scrollbars (only in the iframe) */
    width:100%;
}
.cO { /* this is the iframe */
    height:100%;
    width:100%;
}
.Kj-JD {
    background-color:#C3D9FF;
    border:1px solid #4E5766;
    color:#000000;
    outline:0 none;
    padding:5px;
    position:absolute;
    top:0;
    width:450px;
    z-index:501; /* div stays on top */
}
.Kj-JD-Jh { /* the shadow */
    background-color:#808080;
    left:0;
    position:absolute;
    top:0;
    z-index:500;
}
Sample HTML
<body>
    <iframe class="cO">...</iframe> <!-- the scroll works on the iframe, not the body -->
    <div class="Kj-JD"></div> <!-- outside the iframe -->
    <div class="Kj-JD-Jh" style="opacity: 0.5; width: 1440px; height: 361px;"></div> <!-- black background -->
</body>
To show a div on top I recommend jqModal, it does all the hard work for you.
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