What do you mean by separate files?

If you need to include just an extruder as top for example:

JS CODE:

$(function(){
            $("#extruderTop").buildMbExtruder({
            positionFixed:false,
            position:"top",
            width:350,
            extruderOpacity:1,
            autoCloseTime:0,
            autoOpenTime:1000,
            hidePanelsOnClose:false,
            onExtOpen:function(){},
            onExtContentLoad:function(){},
            onExtClose:function(){}
        });
})

(Change parameters as you need)

DOM CODE:

<div id="extruderTop" class="{title:'extruder top', url:'parts/extruderTop.html'}"></div>

That's all... Bye