Here I have created sample that will help you out.
HTML
<div>
<script type="text/javascript" src="https://code.jquery.com/jquery-2.1.3.js"></script>
<link rel="stylesheet" href='https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css'
media="screen" />
<script type="text/javascript" src='https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/js/bootstrap.min.js'></script>
<script type="text/javascript">
function ShowPopup() {
$('#pnlPopup').modal('show');
return false;
}
function HideModal() {
var modalPopup = $find('mpe');
modalPopup.hide();
$('#pnlPopup').modal('hide');
return false;
}
function pageLoad() {
var modalPopup = $find('mpe');
modalPopup.add_shown(function () {
modalPopup._backgroundElement.addEventListener("click", function () {
modalPopup.hide();
$('#pnlPopup').modal('hide');
});
});
};
</script>
<style type="text/css">
.overrideClass
{
left: 0px !important;
top: 0px !important;
}
</style>
<cc1:ToolkitScriptManager ID="ToolkitScriptManager1" runat="server">
</cc1:ToolkitScriptManager>
<asp:Button ID="btnShow" runat="server" class="btn" Text="Show Modal Popup" OnClientClick="return ShowPopup()">
</asp:Button>
<cc1:ModalPopupExtender ID="ModalPopupExtender1" BehaviorID="mpe" runat="server"
PopupControlID="pnlPopup" TargetControlID="btnShow" BackgroundCssClass="modalBackground">
</cc1:ModalPopupExtender>
<div class="overrideClass">
<asp:Panel ID="pnlPopup" runat="server" class="modal fade overrideClass">
<div class="modal-dialog" role="document">
<div class="modal-content">
<div class="modal-header">
<button type="button" class="close" aria-label="Close" onclick="HideModal()">
<span aria-hidden="true">×</span></button>
<h4 class="modal-title" id="myModalLabel">
Modal title</h4>
</div>
<div class="modal-body">
...
</div>
<div class="modal-footer">
<button type="button" class="btn btn-default" onclick="HideModal()">
Close</button>
<button type="button" class="btn btn-primary" onclick="HideModal()">
Save changes</button>
</div>
</div>
</div>
</asp:Panel>
</div>
</div>
Screenshot