Question

I have put javascript and css pop up in my magento application. I can close the pop up by clicking on close button on pop up, but if user clicks elsewhere(out of pop up window) on the page pop up should be closed.

Answer 1

See this question:
Use jQuery to hide a DIV when the user clicks outside of it

var mouse_is_inside = false;

$(document).ready(function()
{
    $('.form_content').hover(function(){ 
        mouse_is_inside=true; 
    }, function(){ 
        mouse_is_inside=false; 
    });

    $("body").mouseup(function(){ 
        if(! mouse_is_inside) $('.form_wrapper').hide();
    });
});

So you check if the mouse is inside your popup div, and when it is not, you will close it onclick. If you provide some more code we can help you get that set up