I have not registered it with the US copyright office. I have not sent a DMCA take down notice either.
I sent them an email explaining that they need to pay me a licensing fee for use of my footage on their site. As I see it, they owe me the licensing payment, whether they take the footage down now or not, because it's been up on their site already, and they've already used it and benefitted from its use.
Here's the text from the mail I sent:
It has come to my attention that 3 clips of my Killian Videography have been used and are currently being used on your Architecture Effects website located here: (URL hidden)
Please be aware that I retain copyright on this video footage and a licensing fee must be purchased in order to make use of this material on your website.
The licensing fee for web usage by an educational institution is $80 for each clip. I have attached an invoice in the amount of $240 to help expedite payment. Also attached is a screen shot of the webpage indicating the video footage to which I am referring highlighted in red.
Once payment is received I will send you a document for the licensing of this footage for your records. Your prompt attention to this matter will be greatly appreciated.
First, registering your copyrights might be smart. You limit your legal recourse if the works infringed are unregistered.
If you want your videos removed from their location online, your first step will be to file a DMCA takedown notice, pursuant to Section 512 of the Digital Millennium Copyright Act. If the University complies with the takedown notice, your video will be removed from their website.
If there is no compliance, you can file suit and request of the court that a preliminary injunction be issued, barring the University from embedding your copyrighted videos on their site. If the court determines the evidence is sufficient to support an injunction, your video will be removed from the website.
There are some court decisions that have complicated the legality of embedded videos - with some saying it is not copyright infringement to embed a video (comparing embedding to linking) and others saying it can be infringement. Whether you can collect a licensing fee from the University over the embedding on their website of your copyrighted works, therefore, is a question mark.
And, with your description of "clips" as opposed to the entire video, the University may be able to claim a fair use of your material, depending on how much of your work appears and how it appears on their website. If a fair use, the University would not need to license the copyrighted works from you in order to use them (although the University should be crediting the works to you).
You might want to have all of this reviewed by an IP attorney in your area of New York, to determine better where the University stands legally. Most universities are aware of IP laws and what can and cannot be used safely.
With all of that said, your letter to the University is nicely drafted.