You will have to do that in the Dissertations Department (Hochschulschriftenstelle) of the Freie Universität Berlin, a division of the University Library. The Dissertations Department will monitor whether you have met the regulations for the publication of your doctoral thesis and will inform the other university libraries in Germany about the publication. And they will issue a receipt confirming the execution of your publication duties after you have submitted the mandatory copies of your thesis to them.
Please read the information provided on the web pages (guidelines, regulations etc.) of the Dissertations Department very carefully and make sure that the published version of your thesis will meet all the requirements. Otherwise you would run the risk that the copies will be rejected.