I don't want mcafee gateway to scan the PDF file both for inbound and outbound, Is that possible?
If you want to process mail differently, you will need to have a separate policy. Once the second policy is created, you will need to tell it what mail to apply to (remember that inbound and outbound are only reporting flags, they don't make any change to how things are processed), what parts of the policy to inherit from where, and then change the filtering for the files to be different than what was inherited. I'd make a screen shot for you, but I don't have my MEG handy at the moment.
Andy is right, leverage the policy criteria to differintiate between in and outbound messages. I like to use the previous hop's IP to do this. Then you can disable the scan.