If your script can create the files, you should be able to delete tehm using a script as well. Failing that , talk to someone with root privilege.
On a much more significant note, if the owner of the files is root, your webserver is probably running as root. This is a v. bad idea. Apache et all have various well known exploits for gaining route access, particularly if you allow file uploads (it's the reason that v. 4.1.2 was released so quickly).
Details available at:
http://security.e-matters.de/advisories/012002.html
Cheers
Justin