I am not familiar with AutoCAD; does it have such a capability within its own program? Another option might be to use file encryptions (EFS), but you need to thoroughly understand how this works before using it. Make sure you archive your EFS keys! (If you use EFS, make sure neither of you is using the local administrator account.) If one of you logs on using this account, you may become the default recovery agent and could read your encrypted files. PLEASE read all of the info on EFS and make sure you archive your files so you don't lose access to them.
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You can begin your EFS education with the following articles by Roberta:
Dig Deeper on Windows legacy operating systems
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