https://www.cisco.com/c/en/us/td/docs/security/firepower/70/configuration/guide/fpmc-config- guide-v70/transparent_or_routed_firewall_mode_for_firepower_threat_defense.html#id_40010

Reference: https://www.cisco.com/c/en/us/td/docs/security/firepower/650/configuration/guide/fpmc-config-guide-v65/ips_device_deployments_and_configuration.html

To exempt a custom application from being flagged by Cisco Secure Endpoint, the organization must precalculate the hash value of the custom application and add it to the allowed applications list. This process involves creating a hash of the executable file, which uniquely identifies it, and then configuring Cisco Secure Endpoint to recognize this hash as trusted.
Steps:
Calculate the hash value (e.g., SHA-256) of the custom application executable. In the Cisco Secure Endpoint management console, navigate to the policy configuration. Add the calculated hash value to the list of allowed applications or exclusions.
Save and deploy the updated policy.
By adding the hash value to the allowed applications, Cisco Secure Endpoint will recognize the custom application as trusted and will no longer flag it.

Reference:
https://www.cisco.com/c/en/us/support/docs/security/firepower-ngfw/212474-working-with- firepower-threat-defense-f.html