[BDWillis]

I believe the selection you want is "Unused Audio Except Whole Files" in the Regions Bin menu. That will remove all the unused regions from your session, but not the Parent audio files those regions are derived from.

Then when you get the next dialog box, click "Remove", not "Delete". Be aware that "Delete" removes the audio from your disk drive... VERY BAD if that's not what you intended to do!!

Also, you CAN "Remove" the Parent files from the session (those whole files listed in Bold in the Regions Bin) without messing things up... PT will still find the audio as long as you don't "Delete from Disk". (Not trying to talk down to you, but terminology is VERY important in this case, and migrating from one app to another — Logic to Pro Tools — is always confusing in that area.)

Hope this helps, good luck & welcome to PT!!

Warmest Regards,
Brian