Well if your phone has been hacked you should really be looking at backing up your files to a cloud account or a computer and doing a "Hard Reset" on the phone.
However, if the phone isn't hacked and you are just talking for future reference, then you should be good. Make sure you restart (turn off and then back on) the phone after the deleting of the files. Then the system should start using the same space for any new files you put on it. Overwriting what was there before and removing any traces.