Laserfiche in general doesn't have the ability to bring up the kind of "create exception" dialog that you would see in a browser in the case of an untrusted certificate.  Scanning needs the certificate chain to be traceable back to a certificate in the trusted root store.  If this is for public-facing use you have to get a certificate from a CA.  If this is internal, the IT department probably has their own signing key that you could use to replace the cert with a trusted one.  If it's more proof-of-concept or IT doesn't have such a key, you can push your self-signed certificate to the trusted certificate store.

That "create exception" dialog that the browser brings up is just for that application, it doesn't make other applications (like scanning) trust the certificate.