You can do a batch process for multiple PDF files by running an internal batch sequence.

1) Advanced > Document Processing > Batch Processing > New Sequence
2) Enter a name (example: SecurePDF)
3) Select Commands
4) Select Security > Add > Edit
5) Select Password Security
6) Choose Compatibility
7) Choose password to either open the document or restrict editing and printing.
8) Enter password twice (once on main, second for verification)
9) Click Close
10) Click OK > OK
11) Run Sequence > OK
12) Select Files