How to convert a normall ssl in CRT certificate to base64 CER?

Can you copy the files to a windows machine? You don't need openssl to do this conversion, and it looks quite easy.

1. (on windows machine) Double-click on the *.crt file to open it into the certificate display. If it's already imported into certmgr.msc, just browse to it and double click the cert file.
2. Select the Details tab, then select the Copy to file option.
3. Choose next on the Certificate Wizard.
4. Select Base-64 encoded X.509 (.CER) in the File format window, then Next.
5. Finally, enter the path for which to save the new file... make sure it has a .cer extension.

openssl x509 -inform <youchoose> -in certificate.crt -outform <youchoose> -out certificate-out.youchoose

see man openssl x509 for details. You can choose from DER, PEM and NET.

I think you just want to go from DER to PEM (CER is not really an encoding, see here)