It would help to know the names of the files, some are hidden files OS X creates that sometimes become un-hidden and when you delete them, OS X just recreates them again.
1: Make a emergency backup of just your users file folders to a external drive (not only/just TimeMachine) and disconnect this drive.
2: Take all the files out of the Trash and place them on the Desktop.
3: Do the Steps #6 and #12/#13 with OnyX and do all as instructed.
this will repair your user and disk permisisons, reset the caches and let you know if there are more serious issues.
4: Also you can do this as then we can advise of what you need to address in other areas