First, watch this video.
Now I don't know about you, but when I first saw that video my mind was blown. How could someone create a time lapse video in such a busy city without having any signs of life in it. I racked my brain for the little knowledge of time lapses it has, but came up empty. After heavy thinking I decided it was time to turn to the google. I stumbled upon a blog post that helped me understand the time lapse video a lot better, and also gave me inspiration to go out and shoot my own. I'll summarize it below, but if you want to find out more you can do so here.
First, go out and shoot a normal time lapse. Most of the effect is done in post. When shooting the lapse just try to shoot it during a low traffic time.
Then, when editing, you should have enough shots that every part of the traffic area (sidewalks, roads, walkways ect.) should be empty in at least one shot. Layer the photos over each other so that there is never any signs of human life.
Finally just put those layers over the time lapse video and it should work.
For more information follow this link, they do a much better job explaining than I do.
And here is one last time lapse video.