There's many maxscript encrypter out there or here ....I try to make it to support many files at once...just try it....
1. Browse ms file and select many of ms file (right click to append new files)
2. Choose version encoder
3. NF : Make new "Encrypted" folder in current folder and move encrypted files to this new location. You can set it "on" or "off".
4.press "Encrypt" button
Done