You cannot remove a trusted certificate if it has been used to sign a user certificate still present in the wallet. To remove such a trusted certificate, you must first remove the certificates it has signed. Also note, you cannot verify a certificate after its trusted certificate has been removed from your wallet.
Select a trusted certificate listed in the Trusted Certificates tree.
Choose Operations > Remove Trusted Certificate....
A dialog box warns that your user certificate will no longer be verifiable by its recipients if you remove the trusted certificate that was used to sign it.
Choose Yes. The selected trusted certificate is removed from the Trusted Certificates tree.