It's a hard problem to get right. As well as the Safe module the other comment refers to, you may want to look into OS-level permissions.

Assuming Linux, you may be interested in:

• chroot;
• running as a sandbox user-id which owns no files (and is a member of no other groups). (Clear out that user's home dir before each run);
• ulimit and friends to control resource usage

And in this day and age, another good option is to do all this inside a hosted virtual machine. In particular, I know vmware allows you to have a disk which isn't persistent, i.e. all changes are reset on each boot.

Lastly, you said you need to allow users: "to input a perl expression or program and have it run over string."

That's a really unusual requirement. Is there any chance you could tell us why you need to do that? It's possible someone could think of an alternative approach which isn't as risky.