Adding Canonical Links to Files
When you offer files (e.g. PDF files), other sites may copy and host them. If the Google engine detects this, it will stop from indexing your file. You hhave to add a canonical header to avoid this.
The easy way is to use a Typo3 extension for this purpose. You will probably find an extension working for your Typo3 version. Searching the Typo3 extension repository for »canonical« does help.
The hard way is by modifying the .htacess file, if you are using Apache. For me, the following did the trick:
<IfModule mod_headers.c>
# probably other code
# make pdf files canonical
<FilesMatch "\.(pdf)$">
Header add Link expr='href="%{HTTP_HOST}%{REQUEST_URI}"; rel="canonical"'
</FilesMatch>
</IfModule>
Checking if it works
You better should check if your .htaccess file works. I used curl -I (not only on PDF files, but also on other things, to see that they are not touched).