The only way he should have been able to to do is if you have file sharing on, which would make it possible for him to mount your Mac on his desktop.
Open the System Preferences and click on Sharing. Turn off any check boxes in the left column. You may need to unlock the panel at the lower right first.
To restore your bookmarks, you will need to recover them from a backup. Close Safari. For each account, in your backup data, go to the user account's /Library/Safari/ folder. Copy the file Bookmarks.plist to the same location in your user account, overwriting the file already there by the same name. This will need to be for each individual account. Your bookmarks will return to where they were per the last time they were backed up.
If you don't have a backup, you'll have to rebuild your links manually.