You are able to define specific files and folders to exclude from examination and allow for execution. In the Policy you want this to apply to, it's under 'Malware Security Profile' > 'Files/Folders in Allow List'.
Here is the link to the documentation that explains the process:
@Ryan_Saulsbury is correct. You can allow exclusions in the malware profile. You may have to do this for each component -- portable executables, office docs, scans. I've included a few screenshots where you would do this. The screenshots also have examples of the formatting.
PE's and DLL
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