I am new to time lapse and did a timelapse in my Nikon D800E camera. The video is there and I can play it in the camera but how do I extract it as it is not recognized in Lightroom?

You must not use the "time lapse" feature in the camera since it produces a video film right away, instead you must shoot with the intervalometer - either with that in the D800 or - preferably - with an external one to get the single frames.
I'd recommend to get my ebook to learn how all of this works: http://lrtimelapse.com/shop/ebook