so i have bootstrap based site with fixed navigation bar (that follow you around the page at the top) and when i want to show modal popup, it appear behind those navigation bar,
You need to adjust the z-index in your CSS. The z-index for your navigation is higher number than everything else. So to adjust it you need to add a z-index that is higher for your modal popup. the code would look like
For example z-index: 3;
To be able to do this you have to set a position to your popup.
For example position: absolute;
After setting the position you can also adjust the position even more with putting this code in to your CSS
top: 500px; left:500px;
This means that the container you put a absolute position on is moved 500 pixels from the top and 500 pixels from the left.
If you cannot understand what z-index is. I will provide a picture for you.
z-index axis example